suppressMessages(library(minfi))
suppressMessages(library(reshape))
suppressMessages(library(ggplot2))
suppressMessages(library(gridExtra))
suppressMessages(library(RColorBrewer))
suppressMessages(library(here))
suppressMessages(library(binom))
suppressMessages(library(limma))
options(stringsAsFactors = FALSE)
source(here("scripts","00_pretty_plots.R"))
suppressMessages(source(here("scripts","00_heat_scree_plot_generic.R")))
source(here("scripts","00_EM_array_uniform_background.R"))
## Loading required package: splines
# wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.raw.1.zip
# wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.raw.2.zip
# wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.raw.3.zip
# wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.raw.4.zip
# wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.raw.5.zip
# unzip E-MTAB-4957.raw.1.zip
# unzip E-MTAB-4957.raw.2.zip
# unzip E-MTAB-4957.raw.3.zip
# unzip E-MTAB-4957.raw.4.zip
# unzip E-MTAB-4957.raw.5.zip
#wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-4957/E-MTAB-4957.sdrf.txt
path<-"data/published_organoids/E_MTAB_4957"
sampleinfo_organoid <- read.table(here(path, "E-MTAB-4957.sdrf.txt"), header=T, sep="\t")
sampleinfo_organoid<-sampleinfo_organoid[,c(1:15,30:34,38:41)]
#sample info cleanup
sampleinfo_organoid$sentrix<-sapply(1:nrow(sampleinfo_organoid), function(x) strsplit(as.character(sampleinfo_organoid$Assay.Name)[x], "_")[[1]][1])
sampleinfo_organoid$array.id.path <- file.path(here(path), sampleinfo_organoid$Assay.Name)
rgset_organoid <- read.metharray(sampleinfo_organoid$array.id.path, verbose = FALSE)
# Background and dye bias correction with noob thhrough funnorm implemented in minfi
#http://bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html
MSet.illumina <- preprocessFunnorm(rgset_organoid)
## [preprocessFunnorm] Background and dye bias correction with noob
## Loading required package: IlluminaHumanMethylation450kmanifest
## Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
##
## Attaching package: 'IlluminaHumanMethylation450kanno.ilmn12.hg19'
## The following objects are masked from 'package:IlluminaHumanMethylationEPICanno.ilm10b4.hg19':
##
## Islands.UCSC, Locations, Manifest, Other,
## SNPs.132CommonSingle, SNPs.135CommonSingle,
## SNPs.137CommonSingle, SNPs.138CommonSingle,
## SNPs.141CommonSingle, SNPs.142CommonSingle,
## SNPs.144CommonSingle, SNPs.146CommonSingle,
## SNPs.147CommonSingle, SNPs.Illumina
## [preprocessFunnorm] Mapping to genome
## [preprocessFunnorm] Quantile extraction
## [preprocessFunnorm] Normalization
MTAB_organoid_beta<-getBeta(MSet.illumina)
avg_detPval <- colMeans(detectionP(rgset_organoid))
sampleinfo_organoid$det_pval<-avg_detPval
print("detection pval")
## [1] "detection pval"
ggplot(sampleinfo_organoid)+geom_boxplot(aes(as.factor(sentrix), det_pval, fill=as.factor(sentrix)), outlier.shape = NA)+
geom_point(aes(as.factor(sentrix), det_pval, group=Assay.Name, fill=as.factor(sentrix)), shape=21, color="black",
position = position_jitter(w = 0.25))+theme_bw()+theme(axis.text.x=element_text(angle = 45, vjust = 1, hjust=1))+
xlab("Sentrix ID")+ylab("Mean Detection P Value")+guides(fill=FALSE)+ylim(0,0.008)
ggsave(here("figs","MTAB4957_detection_pvalue.pdf"), width=6, height=5)
ggsave(here("figs/jpeg","MTAB4957_detection_pvalue.jpeg"), width=6, height=5)
Beta distribution before and after normalization
beta_raw<-getBeta(rgset_organoid)
betas<-getBeta(MSet.illumina)
Beta_melted<- melt(betas)
Beta_melted_raw<- melt(beta_raw)
#remove NAs before plotting (otherwise get many non-inifnite warnings)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
Beta_Plot_raw<-Beta_melted_raw[which(!(is.na(Beta_melted_raw$value))),]
#add meta
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,sampleinfo_organoid, by.x="ID", by.y="Assay.Name")
colnames(Beta_Plot_raw)<-c("CpG","ID","Beta")
Beta_Plot_raw<-merge(Beta_Plot_raw,sampleinfo_organoid, by.x="ID", by.y="Assay.Name")
dis1<-ggplot(Beta_Plot, aes(Beta, group=as.character(ID), color=as.character(Characteristics.sampling.site.)))+
geom_density()+theme_bw()+xlab("DNAm Beta Value")
dis2<-ggplot(Beta_Plot_raw, aes(Beta, group=as.character(ID), color=as.character(Characteristics.sampling.site.)))+
geom_density()+theme_bw()+xlab("DNAm Beta Value")
ggsave(here("figs","MTAB4957_beta_distribution.pdf"), grid.arrange(dis1, dis2),w=20, h=5)
ggsave(here("figs/jpeg","MTAB4957_beta_distribution.jpeg"), grid.arrange(dis1, dis2), w=20, h=5)
MTAB_organoid_beta <- MTAB_organoid_beta[!grepl("rs",rownames(MTAB_organoid_beta)), ]
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"\nProbes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134\nProbes available: 485512"
# https://emea.support.illumina.com/downloads/humanmethylation450_15017482_v1-2_product_files.html
anno_450k<-read.csv(here("data","HumanMethylation450_15017482_v1-2.csv"), skip=7)
anno_450k<-anno_450k[match(rownames(MTAB_organoid_beta),anno_450k$IlmnID),]
identical(rownames(MTAB_organoid_beta), anno_450k$IlmnID)
## [1] TRUE
MTAB_organoid_beta<-MTAB_organoid_beta[which(!(anno_450k$CHR%in%c('X','Y'))),]
filt_sex<-nrow(MTAB_organoid_beta)
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"Probes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134Probes available: 473864"
Some probes have been found to cross-hybridize with other chromosomes (Price et al. 2013 Epigenetics). https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16304
price<-read.table(here("data","GPL16304-47833.txt"), sep='\t', header=T, skip=22)
price<-price[match(rownames(MTAB_organoid_beta),price$ID),]
cross_hyb<-price[which(price$XY_Hits=="XY_YES" | price$Autosomal_Hits=="A_YES"),]
MTAB_organoid_beta<-MTAB_organoid_beta[which(!(rownames(MTAB_organoid_beta)%in%cross_hyb$ID)),]
filt_cross<-nrow(MTAB_organoid_beta)
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"\nProbes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134\nProbes available: 433274"
Polymorphic probes
SnpatCpG<-price[which(price$Target.CpG.SNP!=""),]
MTAB_organoid_beta<-MTAB_organoid_beta[which(!(rownames(MTAB_organoid_beta)%in%SnpatCpG$ID)),]
filt_poly<-nrow(MTAB_organoid_beta)
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"\nProbes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134\nProbes available: 415080"
Remove probes with high NA count
na_count_probe <-sapply(1:nrow(MTAB_organoid_beta), function(y) length(which(is.na(MTAB_organoid_beta[y,]))))
na_count_probe_good<-which(na_count_probe<(ncol(MTAB_organoid_beta)*0.05))
MTAB_organoid_beta<-MTAB_organoid_beta[na_count_probe_good,]
filt_bead<-nrow(MTAB_organoid_beta)
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"\nProbes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134\nProbes available: 415080"
Remove probes with high detection p value across samples, and any samples with many high detection p value probes
detP <- detectionP(rgset_organoid)
failed <- detP>0.05
bad_det_p<-names(which(rowMeans(failed)>0.01))
bad_det_psamp<-names(which(colMeans(failed)>0.01))
MTAB_organoid_beta<-MTAB_organoid_beta[which(!(rownames(MTAB_organoid_beta)%in%bad_det_p)),]
MTAB_organoid_beta<-MTAB_organoid_beta[,which(!(colnames(MTAB_organoid_beta)%in%bad_det_psamp))]
filt_detp<-nrow(MTAB_organoid_beta)
print(paste("Samples available: ",ncol(MTAB_organoid_beta),"\nProbes available: ",nrow(MTAB_organoid_beta),sep=""))
## [1] "Samples available: 134\nProbes available: 409528"
sampleinfo_organoid<-sampleinfo_organoid[,c(1:16,24:27)]
identical(colnames(MTAB_organoid_beta),sampleinfo_organoid$Assay.Name)
## [1] TRUE
head(sampleinfo_organoid)
## Source.Name Material.Type Characteristics.organism.
## 1 P1 organism part Homo sapiens
## 2 P2 organism part Homo sapiens
## 3 P3 organism part Homo sapiens
## 4 P4 organism part Homo sapiens
## 5 P5 organism part Homo sapiens
## 6 P6 organism part Homo sapiens
## Characteristics.individual. Characteristics.cell.type.
## 1 P1 organism part
## 2 P2 organism part
## 3 P3 organism part
## 4 P4 organism part
## 5 P5 organism part
## 6 P6 organism part
## Characteristics.biosource.type. Characteristics.developmental.stage.
## 1 organism part juvenile stage
## 2 organism part juvenile stage
## 3 organism part juvenile stage
## 4 organism part juvenile stage
## 5 organism part juvenile stage
## 6 organism part juvenile stage
## Characteristics.sampling.site. Characteristics.age. Unit.time.unit.
## 1 sigmoid colon 5 to 15 year
## 2 sigmoid colon 5 to 15 year
## 3 sigmoid colon 6 to 15 year
## 4 sigmoid colon 7 to 15 year
## 5 sigmoid colon 8 to 15 year
## 6 sigmoid colon 9 to 15 year
## Term.Source.REF Term.Accession.Number Characteristics.sex.
## 1 EFO UO_0000036 female
## 2 EFO UO_0000036 male
## 3 EFO UO_0000036 male
## 4 EFO UO_0000036 male
## 5 EFO UO_0000036 male
## 6 EFO UO_0000036 male
## Characteristics.passage. Comment..basename. Assay.Name
## 1 not applicable 5831583005_R01C01 5831583005_R01C01
## 2 not applicable 5831583005_R02C01 5831583005_R02C01
## 3 not applicable 5831583005_R03C01 5831583005_R03C01
## 4 not applicable 5831583005_R04C01 5831583005_R04C01
## 5 not applicable 5831583005_R05C01 5831583005_R05C01
## 6 not applicable 5831583005_R06C01 5831583005_R06C01
## Factor.Value..block. sentrix
## 1 5 5831583005
## 2 5 5831583005
## 3 5 5831583005
## 4 5 5831583005
## 5 5 5831583005
## 6 5 5831583005
## array.id.path
## 1 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R01C01
## 2 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R02C01
## 3 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R03C01
## 4 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R04C01
## 5 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R05C01
## 6 /nfs/research1/zerbino/redgar/organoid_passage_DNAm/data/published_organoids/E_MTAB_4957/5831583005_R06C01
## det_pval
## 1 0.0009280434
## 2 0.0002483935
## 3 0.0003242456
## 4 0.0002260101
## 5 0.0002923051
## 6 0.0004080649
sampleinfo_ped_primary<-sampleinfo_organoid[which(sampleinfo_organoid$Characteristics.developmental.stage.=="juvenile stage" & sampleinfo_organoid$Characteristics.biosource.type.=="purified cell"),]
print(paste("Primary pediatric samples available: ",nrow(sampleinfo_ped_primary), sep=""))
## [1] "Primary pediatric samples available: 35"
# Three samples are the non-epithelial portion
sampleinfo_ped_primary<-sampleinfo_ped_primary[-grep("non-epithelial",sampleinfo_ped_primary$Characteristics.cell.type.),]
organoid_ped_primary<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_ped_primary$Assay.Name)]
identical(colnames(organoid_ped_primary),sampleinfo_ped_primary$Assay.Name)
## [1] TRUE
print(paste("Primary samples available: ",nrow(sampleinfo_ped_primary), sep=""))
## [1] "Primary samples available: 32"
sampleinfo_fetal_primary<-sampleinfo_organoid[which(sampleinfo_organoid$Characteristics.developmental.stage.=="fetal stage" & sampleinfo_organoid$Characteristics.biosource.type.=="purified cell"),]
print(paste("Primary fetal samples available: ",nrow(sampleinfo_fetal_primary), sep=""))
## [1] "Primary fetal samples available: 11"
organoid_fetal_primary<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_fetal_primary$Assay.Name)]
identical(colnames(organoid_fetal_primary),sampleinfo_fetal_primary$Assay.Name)
## [1] TRUE
print(paste("Primary samples available: ",nrow(sampleinfo_fetal_primary), sep=""))
## [1] "Primary samples available: 11"
sampleinfo_organoid<-sampleinfo_organoid[which(sampleinfo_organoid$Characteristics.biosource.type.=="organoid"),]
MTAB_organoid_beta<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid$Assay.Name)]
identical(colnames(MTAB_organoid_beta),sampleinfo_organoid$Assay.Name)
## [1] TRUE
print(paste("Organoid samples available: ",nrow(sampleinfo_organoid), sep=""))
## [1] "Organoid samples available: 82"
sampleinfo_organoid$passage.or.rescope.no_numeric<-as.factor(as.character(sampleinfo_organoid$Characteristics.passage.))
levels(sampleinfo_organoid$passage.or.rescope.no_numeric)<-c(1,11,12,14,18,2,21,23,3,4,5,6,7,8,9)
sampleinfo_organoid$passage.or.rescope.no_numeric<-as.numeric(as.character(sampleinfo_organoid$passage.or.rescope.no_numeric))
sample_ID to include patient and tissue
sampleinfo_organoid$sample_ID<-paste(sampleinfo_organoid$Characteristics.individual., sampleinfo_organoid$Characteristics.sampling.site.)
remove AP as it seems to indicate a mixture of passages (i.e P1AP6)? These aen’t mentioned in manscript?
sampleinfo_organoid<-sampleinfo_organoid[-grep("AP",sampleinfo_organoid$Source.Name),]
Unclear what GM and IM are but it seems like only 281 was under these conditions, so will exclude to be safe
sampleinfo_organoid<-sampleinfo_organoid[-grep("281",sampleinfo_organoid$Source.Name),]
tidy condition
sampleinfo_organoid$condition<-NA
need to grep for WT and Clone B
sampleinfo_organoid$condition[grep("WT",sampleinfo_organoid$Source.Name)]<-"WT"
sampleinfo_organoid$condition[grep("Clone B|CloneB",sampleinfo_organoid$Source.Name)]<-"KO"
DM seems to be differenitated and SCM is maybe undifferentiated
sampleinfo_organoid$condition[grep("SCM",sampleinfo_organoid$Source.Name)]<-"SCM"
sampleinfo_organoid$condition[grep("DM",sampleinfo_organoid$Source.Name)]<-"DM4d"
print(paste("Organoid samples available: ",nrow(sampleinfo_organoid), sep=""))
## [1] "Organoid samples available: 70"
# match the DNAm data
MTAB_organoid_beta<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid$Assay.Name)]
identical(colnames(MTAB_organoid_beta),sampleinfo_organoid$Assay.Name)
## [1] TRUE
Individuals “212” “223” “224” “225” “369” are in both studies. The organoids from these individuals will be removed from the differential DNAm analysis, but visulized later to show the patterns occur across array type Saving them for later integration
sampleinfo_organoid_paired<-sampleinfo_organoid[grep("212|223|224",sampleinfo_organoid$Characteristics.individual.),]
MTAB4957_beta_for_paird<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid_paired$Assay.Name)]
identical(colnames(MTAB4957_beta_for_paird), sampleinfo_organoid_paired$Assay.Name)
## [1] TRUE
print(paste("Organoid samples available: ",nrow(sampleinfo_organoid_paired), sep=""))
## [1] "Organoid samples available: 16"
load the EPIC organoids
load(here("data","beta_organoids.RData"))
intersect(sampleinfo_organoid$Characteristics.individual., epic.organoid$case.no)
## [1] "212" "223" "224" "225" "369"
369 and 225 are run at identical passages in both cohorts so all samples will be removed.
sampleinfo_organoid[grep("369",sampleinfo_organoid$Characteristics.individual.),c(1,4,8,9,13,21,22)]
## Source.Name Characteristics.individual.
## 105 369 TI P3 SCM 369
## 106 369 TI P3 DM4d 369
## 108 369 SC P3 SCM 369
## 110 369 SC P3 DM4d 369
## Characteristics.sampling.site. Characteristics.age.
## 105 terminal ileum 9
## 106 terminal ileum 9
## 108 sigmoid colon 9
## 110 sigmoid colon 9
## Characteristics.sex. passage.or.rescope.no_numeric sample_ID
## 105 male 3 369 terminal ileum
## 106 male 3 369 terminal ileum
## 108 male 3 369 sigmoid colon
## 110 male 3 369 sigmoid colon
epic.organoid[grep("369",epic.organoid$case.no),c(1,5,17, 9, 10)]
## case.no sample.site passage.or.rescope.no_numeric sex age
## 22 369 SC 3 M 9
## 23 369 TI 3 M 9
sampleinfo_organoid<-sampleinfo_organoid[-grep("369|225",sampleinfo_organoid$Characteristics.individual.),]
212,223 and 224 have organoids at passages only used in MTAB-4957. So organoids that are included at the same passage will be removed.
remove_sampleID<-c("212 SC P6","212 TI P6","223 SC P2","223 TI P2","224 SC P3","224 TI P2")
sampleinfo_organoid<-sampleinfo_organoid[which(!(sampleinfo_organoid$Source.Name%in%remove_sampleID)),]
print(paste("Organoid samples available: ",nrow(sampleinfo_organoid), sep=""))
## [1] "Organoid samples available: 58"
# match the DNAm data
MTAB_organoid_beta<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid$Assay.Name)]
identical(colnames(MTAB_organoid_beta),sampleinfo_organoid$Assay.Name)
## [1] TRUE
pca_res <- prcomp(t(MTAB_organoid_beta))
Loadings<-as.data.frame(pca_res$x)
vars <- pca_res$sdev^2
Importance<-vars/sum(vars)
meta_categorical <- sampleinfo_organoid[, c(4,7,8,13,17,18)] # input column numbers in meta that contain categorical variables
meta_continuous <- sampleinfo_organoid[, c(9,21)] # input column numbers in meta that contain continuous variables
colnames(meta_categorical) <- c("Individual", "Developmental Stage","Sample Site","Sex","Block","Sentrix ID")
colnames(meta_continuous) <- c("Age", "Passage")
meta_continuous$Age<-as.numeric(meta_continuous$Age)
meta_categorical$Block<-as.factor(meta_categorical$Block)
ord<-1:length(c(colnames(meta_categorical),colnames(meta_continuous)))
PCs_to_view<-10
suppressWarnings(heat_scree_plot(Loadings, Importance, 2.5, 2.7))
## PC vs PC plot
Loadings$Assay.Name<-rownames(Loadings)
Loadings_meta<-merge(Loadings, sampleinfo_organoid, by="Assay.Name")
ggplot(Loadings_meta, aes(PC1, PC2, fill=Characteristics.developmental.stage.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (29%)")+ylab("PC2 (10%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
ggplot(Loadings_meta, aes(PC1, PC2, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (29%)")+ylab("PC2 (10%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
ggplot(Loadings_meta, aes(PC2, PC3, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC2 (10%)")+ylab("PC3 (8%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
pc_plt<-ggplot(Loadings_meta, aes(PC2, PC3, fill=as.factor(passage.or.rescope.no_numeric),color=Characteristics.developmental.stage.))+geom_line(aes(PC2,PC3, group=sample_ID), color="lightgrey")+#, color=sampling.time.point
geom_point(shape=21,size=3)+#
theme_bw()+xlab("PC2 (10%)")+ylab("PC3 (8%)")+th+theme(axis.text = element_text(size=12),axis.title = element_text(size=14))+
scale_fill_manual(values=pass_col,name="Passage\nNumber")+scale_color_manual(values=c("black","white","black"))
legend<-ggplot(sampleinfo_organoid, aes(as.factor(-passage.or.rescope.no_numeric), fill=as.factor(passage.or.rescope.no_numeric)))+geom_bar(color="black")+
theme_bw()+theme(legend.position = "none", axis.text.y = element_blank(),
axis.title.y = element_blank(),
axis.ticks.y = element_blank(),
legend.title=element_text(size=10),
legend.text=element_text(size=8))+
coord_flip()+
scale_fill_manual(values=pass_col,name="Passage\nNumber")+th
r <- ggplot() + theme_void()
grid.arrange(pc_plt,arrangeGrob(r,legend,r, heights=c(0.6,1.25,0.4)), ncol=2, widths=c(7,1))
High passage fetal toward older organoids?
ggplot(Loadings_meta, aes(PC1, PC2, fill=as.factor(passage.or.rescope.no_numeric), color=Characteristics.developmental.stage.))+geom_line(aes(PC1,PC2, group=sample_ID), color="lightgrey")+#, color=sampling.time.point
geom_point(shape=21,size=3)+#
theme_bw()+xlab("PC2 (10%)")+ylab("PC3 (8%)")+th+theme(axis.text = element_text(size=12),axis.title = element_text(size=14))+
scale_fill_manual(values=pass_col,name="Passage\nNumber")+scale_color_manual(values=c("black","white","black"))
sampleinfo_organoid_notfetal<-sampleinfo_organoid[which(sampleinfo_organoid$Characteristics.biosource.type.=="organoid" & sampleinfo_organoid$Characteristics.developmental.stage.!="fetal stage"),]
MTAB_organoid_beta_notfetal<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid_notfetal$Assay.Name)]
identical(colnames(MTAB_organoid_beta_notfetal),sampleinfo_organoid_notfetal$Assay.Name)
## [1] TRUE
pca_res <- prcomp(t(MTAB_organoid_beta_notfetal))
Loadings<-as.data.frame(pca_res$x)
vars <- pca_res$sdev^2
Importance<-vars/sum(vars)
meta_categorical <- sampleinfo_organoid_notfetal[, c(4,7,8,13,17,18)] # input column numbers in meta that contain categorical variables
meta_continuous <- sampleinfo_organoid_notfetal[, c(9,21)] # input column numbers in meta that contain continuous variables
colnames(meta_categorical) <- c("Individual", "Developmental Stage","Sample Site","Sex","Block","Sentrix ID")
colnames(meta_continuous) <- c("Age", "Passage")
meta_continuous$Age<-as.numeric(meta_continuous$Age)
meta_categorical$Block<-as.factor(meta_categorical$Block)
ord<-1:length(c(colnames(meta_categorical),colnames(meta_continuous)))
PCs_to_view<-10
suppressWarnings(heat_scree_plot(Loadings, Importance, 2.5, 2.7))
## PC vs PC plot
Loadings$Assay.Name<-rownames(Loadings)
Loadings_meta<-merge(Loadings, sampleinfo_organoid_notfetal, by="Assay.Name")
Sample Site
ggplot(Loadings_meta, aes(PC1, PC2, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (19%)")+ylab("PC2 (13%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
Condition
ggplot(Loadings_meta, aes(PC1, PC2, fill=condition))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (19%)")+ylab("PC2 (13%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
Sample Site PC2/3
ggplot(Loadings_meta, aes(PC2, PC3, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC2 (13%)")+ylab("PC3 (10%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
Sample Site PC3/4
ggplot(Loadings_meta, aes(PC3, PC4, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC3 (10%)")+ylab("PC4 (6%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
pc_plt<-ggplot(Loadings_meta, aes(PC2, PC3, fill=as.factor(passage.or.rescope.no_numeric)))+geom_line(aes(PC2,PC3, group=sample_ID), color="lightgrey")+#, color=sampling.time.point
geom_point(shape=21,size=3)+#
theme_bw()+xlab("PC2 (10%)")+ylab("PC3 (8%)")+th+theme(axis.text = element_text(size=12),axis.title = element_text(size=14))+
scale_fill_manual(values=pass_col,name="Passage\nNumber")+scale_color_manual(values=c("black","white","black"))
legend<-ggplot(sampleinfo_organoid_notfetal, aes(as.factor(-passage.or.rescope.no_numeric), fill=as.factor(passage.or.rescope.no_numeric)))+geom_bar(color="black")+
theme_bw()+theme(legend.position = "none", axis.text.y = element_blank(),
axis.title.y = element_blank(),
axis.ticks.y = element_blank(),
legend.title=element_text(size=10),
legend.text=element_text(size=8))+
coord_flip()+
scale_fill_manual(values=pass_col,name="Passage\nNumber")+th
r <- ggplot() + theme_void()
grid.arrange(pc_plt,arrangeGrob(r,legend,r, heights=c(0.6,1.25,0.4)), ncol=2, widths=c(7,1))
Variation<-function(x) {quantile(x, c(0.9), na.rm=T)[[1]]-quantile(x, c(0.1), na.rm=T)[[1]]}
Mval<-function(beta) log2(beta/(1-beta))
MTAB4957_mval= apply(MTAB_organoid_beta_notfetal, 1, Mval) # need mvalues for combat
MTAB4957_mval = as.data.frame(MTAB4957_mval)
MTAB4957_mval = t(MTAB4957_mval)
ref_range_dnam<-sapply(1:nrow(MTAB4957_mval), function(x) Variation(MTAB4957_mval[x,]))
dim(MTAB4957_beta_VeryVariable<-MTAB_organoid_beta_notfetal[which(ref_range_dnam>=2.75),])# 47924
## [1] 47924 30
## Beta distribution plot
Beta_melted<- melt(MTAB4957_beta_VeryVariable)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,sampleinfo_organoid_notfetal, by.x="ID", by.y="Assay.Name")
Beta_Plot$passage.or.rescope.no_numeric.factor <- factor(Beta_Plot$passage.or.rescope.no_numeric, levels = c(11,9,8,6,4,3,2,1))
ggplot(Beta_Plot, aes(Beta,color=passage.or.rescope.no_numeric.factor))+
geom_density(size=1)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=pass_col, name="Passage\nNumber")+th+theme(legend.text = element_text(size=7),
legend.title = element_text(size=10),
legend.key.size = unit(0.7,"line"))
To view the beta distributions we will also include a line for the 32 primary samples to compare each passage to primary
MTAB4957_mval= apply(organoid_ped_primary, 1, Mval) # need mvalues for combat
MTAB4957_mval = as.data.frame(MTAB4957_mval)
MTAB4957_mval = t(MTAB4957_mval)
ref_range_dnam_primary<-sapply(1:nrow(MTAB4957_mval), function(x) Variation(MTAB4957_mval[x,]))
dim(organoid_ped_primary_VeryVariable<-organoid_ped_primary[rev(order(ref_range_dnam_primary)),])
## [1] 409528 32
Include the same number of vairable CpGs as organoids varible. So take the 41961 most variable
dim(organoid_ped_primary_VeryVariable<-organoid_ped_primary_VeryVariable[1:41961 ,])
## [1] 41961 32
Beta_melted_MTAB_primary<- melt(organoid_ped_primary_VeryVariable)
Beta_Plot_MTAB_primary<-Beta_melted_MTAB_primary[which(!(is.na(Beta_melted_MTAB_primary$value))),]
colnames(Beta_Plot_MTAB_primary)<-c("CpG","ID","Beta")
Beta_Plot_MTAB_primary<-merge(Beta_Plot_MTAB_primary,sampleinfo_ped_primary, by.x="ID", by.y="Assay.Name")
Beta_plot_primary<-Beta_Plot_MTAB_primary[,c(1:3)]
Beta_plot_primary$passage.or.rescope.no_numeric<-0
Beta_Plot<-Beta_Plot[,c(1:3,23)]
Beta_Plot_combined<-rbind(Beta_plot_primary,Beta_Plot)
Beta_Plot_combined$passage.or.rescope.no_numeric.factor <- factor(Beta_Plot_combined$passage.or.rescope.no_numeric, levels = c(11,9,8,6,4,3,2,1,0))
ggplot(Beta_Plot_combined, aes(Beta,color=as.factor(passage.or.rescope.no_numeric.factor)))+
geom_density(size=1)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=pass_col, name="Passage\nNumber")+th+theme(legend.text = element_text(size=7),
legend.title = element_text(size=10),
legend.key.size = unit(0.7,"line"))
ggsave(here("figs","MTAB4957_beta_notfetal_with_primary.pdf"),width = 3.75, height = 2.5)
ggsave(here("figs/jpeg","MTAB4957_beta_notfetal_with_primary.jpeg"), width = 3.75, height = 2.5)
These are just the from the individuals not shared across studies
sampleinfo_organoid_notfetal$sample.site<-as.factor(sampleinfo_organoid_notfetal$Characteristics.sampling.site.)
levels(sampleinfo_organoid_notfetal$sample.site)<-c("SC","TI")
sampleinfo_organoid_notfetal$sample_ID<-paste(sampleinfo_organoid_notfetal$Characteristics.individual., sampleinfo_organoid_notfetal$sample.site)
sampleinfo_organoid_paired_unique<-sampleinfo_organoid_notfetal[which(sampleinfo_organoid_notfetal$sample_ID%in%sampleinfo_organoid_notfetal$sample_ID[duplicated(sampleinfo_organoid_notfetal$sample_ID)]),]
MTAB4957.organoid_paired<-do.call(rbind,lapply(1:length(unique(sampleinfo_organoid_paired_unique$sample_ID)), function(x){
sample<-unique(sampleinfo_organoid_paired_unique$sample_ID)[x]
samp<-sampleinfo_organoid_paired_unique[sampleinfo_organoid_paired_unique$sample_ID==sample,]
samp<-samp[order(samp$passage.or.rescope.no_numeric),]
samp$hilo<-as.factor(samp$passage.or.rescope.no_numeric)
if(length(levels(samp$hilo))==2){levels(samp$hilo)<-c("lower","higher")}else{
if(length(levels(samp$hilo))==3){levels(samp$hilo)<-c("lower","higher","highest")}else{
if(length(levels(samp$hilo))==4){levels(samp$hilo)<-c("lowest","lower","higher","highest")}else{samp$hilo<-NA}
}
}
samp
}))
MTAB4957.organoid_paired<-MTAB4957.organoid_paired[which(!is.na(MTAB4957.organoid_paired$hilo)),]
## will include 224 in the combined plot with its passage 2,3 samples that were on the epic
MTAB4957.organoid_paired<-MTAB4957.organoid_paired[-(grep("224", MTAB4957.organoid_paired$Source.Name)),]
MTAB4957_beta_VeryVariable_paird<-MTAB4957_beta_VeryVariable[,which(sampleinfo_organoid_notfetal$sample_ID%in%MTAB4957.organoid_paired$sample_ID)]
Beta_melted<- melt(MTAB4957_beta_VeryVariable_paird)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,MTAB4957.organoid_paired, by.x="ID", by.y="Assay.Name")
labels<-as.data.frame(tapply(MTAB4957.organoid_paired$passage.or.rescope.no_numeric, MTAB4957.organoid_paired$sample_ID, function(x) paste(x, collapse=", ")))
colnames(labels)<-"passge"
labels$sample_ID<-rownames(labels)
ggplot()+
geom_density(aes(Beta,color=hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values = c ("#9ecae1", "#225ea8", "#081d58"), name="Relative\nPassage\nLevel within\nPatient")+facet_wrap(~sample_ID, nrow=1)+
geom_text(aes(0.75, 2.75, label=passge), data=labels, color="grey20")+th+theme(strip.text = element_text(size = 10),
axis.text=element_text(size=4),
panel.spacing = unit(0.7, "lines"))+th+
scale_x_continuous(breaks = c(0,0.5,1))
ggsave(here("figs","MTAB4957_beta_paired_notfetal.pdf"),width = 5, height = 2.2)
ggsave(here("figs/jpeg","MTAB4957_beta_paired_notfetal.jpeg"), width = 5, height = 2.2)
these are individuals present in both studies
intersect(sampleinfo_organoid_paired$Characteristics.individual., epic.organoid$case.no)
## [1] "212" "223" "224"
organoid_Mval = apply(organoid_beta, 1, Mval) # need mvalues for combat
organoid_Mval = as.data.frame(organoid_Mval)
organoid_Mval = t(organoid_Mval)
ref_range_dnam<-sapply(1:nrow(organoid_Mval), function(x) Variation(organoid_Mval[x,]))
organoid_beta_VeryVariable<-organoid_beta[which(ref_range_dnam>=2.75),]# 51545
“212” “223” “224” in both studes
epic.organoid_paired<-epic.organoid[grep("212|223|224",epic.organoid$case.no),]
MTAB4957_beta_VeryVariable_paird<-MTAB4957_beta_for_paird[which(rownames(MTAB4957_beta_for_paird)%in%rownames(MTAB4957_beta_VeryVariable)),]
identical(colnames(MTAB4957_beta_VeryVariable_paird), as.character(sampleinfo_organoid_paired$Assay.Name))
## [1] TRUE
epic.organoid_beta_VeryVariable_paird<-organoid_beta_VeryVariable[,which(colnames(organoid_beta_VeryVariable)%in%epic.organoid_paired$array.id)]
epic.organoid_beta_VeryVariable_paird<-epic.organoid_beta_VeryVariable_paird[,match(epic.organoid_paired$array.id,colnames(epic.organoid_beta_VeryVariable_paird))]
identical(colnames(epic.organoid_beta_VeryVariable_paird), as.character(epic.organoid_paired$array.id))
## [1] TRUE
epic.organoid_paired$Study<-"Original Organoids"
sampleinfo_organoid_paired$Study<-"E-MTAB-4957"
sampleinfo_organoid_paired$sample_ID<-gsub(" sigmoid colon", " SC",sampleinfo_organoid_paired$sample_ID)
sampleinfo_organoid_paired$sample_ID<-gsub(" terminal ileum", " TI",sampleinfo_organoid_paired$sample_ID)
colnames(sampleinfo_organoid_paired)[c(4,16)]<-c("case.no","array.id")
samplinfo_paired_combined<-rbind(epic.organoid_paired[,c(1,2,14,17,18)],sampleinfo_organoid_paired[,c(4,16,22,21,24)])
variable_beta_combined<-merge(epic.organoid_beta_VeryVariable_paird,MTAB4957_beta_VeryVariable_paird, by="row.names")
variable_beta_combined$Row.names<-NULL
identical(colnames(variable_beta_combined), as.character(samplinfo_paired_combined$array.id))
## [1] TRUE
samplinfo_paired_combined<-do.call(rbind,lapply(1:length(unique(samplinfo_paired_combined$sample_ID)), function(x){
sample<-unique(samplinfo_paired_combined$sample_ID)[x]
samp<-samplinfo_paired_combined[samplinfo_paired_combined$sample_ID==sample,]
samp<-samp[order(samp$passage.or.rescope.no_numeric),]
samp$hilo<-as.factor(samp$passage.or.rescope.no_numeric)
if(length(levels(samp$hilo))==2){levels(samp$hilo)<-c("lower","higher")}else{
if(length(levels(samp$hilo))==3){levels(samp$hilo)<-c("lower","higher","highest")}else{
if(length(levels(samp$hilo))==4){levels(samp$hilo)<-c("lowest","lower","higher","highest")}else{samp$hilo<-NA}
}
}
samp
}))
Beta_melted<- melt(variable_beta_combined)
## No id variables; using all as measure variables
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("ID","Beta")
Beta_Plot<-merge(Beta_Plot,samplinfo_paired_combined, by.x="ID", by.y="array.id")
Beta_Plot$hilo_epic<-paste(Beta_Plot$hilo,"\n", Beta_Plot$Study, sep="")
Beta_Plot$hilo_epic<-factor(Beta_Plot$hilo_epic, levels=c("lower\nOriginal Organoids", "lower\nE-MTAB-4957", "higher\nE-MTAB-4957", "highest\nE-MTAB-4957"))
labels<-as.data.frame(tapply(samplinfo_paired_combined$passage.or.rescope.no_numeric, list(samplinfo_paired_combined$sample_ID,samplinfo_paired_combined$Study), function(x) paste(x, collapse=", ")))
labels$sample_ID<-rownames(labels)
colnames(labels)<-c("MTAB","OG","sample_ID")
labels$MTAB<-paste("E-MTAB-4957: ", labels$MTAB, sep="")
labels$OG<-paste("Original Organoid: ", labels$OG, sep="")
ggplot()+
geom_density(aes(Beta,color=hilo_epic, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values = c ("#ef3b2c", "#9ecae1","#225ea8","#081d58"), name="Relative\nPassage\nLevel within\nPatient")+facet_wrap(~sample_ID, nrow=3)+
geom_text(aes(0.5, 2.65, label=MTAB), data=labels, color="grey20", size=2.75)+
geom_text(aes(0.5, 2.35, label=OG), data=labels, color="grey20", size=2.75)+
th+theme(strip.text = element_text(size = 12),
axis.text=element_text(size=10),
panel.spacing = unit(0.7, "lines"),
legend.text=element_text(size=9.5),
legend.title=element_text(size=12))+ scale_x_continuous(breaks = c(0,0.5,1))
ggsave(here("figs","MTAB4957_EPIC_beta_paired.pdf"),width = 6, height = 6)
ggsave(here("figs/jpeg","MTAB4957_EPIC_beta_paired.jpeg"), width = 6, height = 6)
sampleinfo_organoid_notfetal$thresholded_prior_I<-sapply(1:nrow(sampleinfo_organoid_notfetal), function(x){
passage<-paste("passage: ",sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric[x],"\nIndividual: ", sampleinfo_organoid_notfetal$case.no[x],"\nThreshold: " ,sampleinfo_organoid_notfetal$thresholded_passage[x], sep="")
converted<-as.numeric(round(MTAB4957_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
res$prior_I
})
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -270103.38 0.60 0.23 0.15 0.02 0.16
## [7] 0.10 0.87 0.04 0.51 0.05
## [1] -265615.03 0.64 0.20 0.12 0.03 0.18
## [7] 0.11 0.85 0.04 0.51 0.05
## [1] -264789.93 0.66 0.19 0.11 0.04 0.20
## [7] 0.11 0.84 0.04 0.52 0.05
## [1] -264484.65 0.67 0.18 0.10 0.04 0.21
## [7] 0.12 0.83 0.05 0.52 0.05
## [1] -264372.38 0.67 0.18 0.10 0.05 0.22
## [7] 0.13 0.83 0.05 0.52 0.05
## [1] -264345.26 0.67 0.18 0.10 0.05 0.22
## [7] 0.13 0.82 0.05 0.53 0.05
## [1] -264354.33 0.66 0.18 0.10 0.06 0.23
## [7] 0.13 0.82 0.05 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267948.50 0.57 0.28 0.12 0.02 0.14
## [7] 0.11 0.87 0.04 0.50 0.05
## [1] -265300.54 0.62 0.26 0.09 0.03 0.15
## [7] 0.12 0.85 0.04 0.51 0.04
## [1] -264779.32 0.63 0.25 0.08 0.04 0.16
## [7] 0.13 0.84 0.05 0.51 0.04
## [1] -264588.26 0.64 0.25 0.07 0.04 0.17
## [7] 0.14 0.83 0.05 0.51 0.04
## [1] -264520.21 0.64 0.25 0.07 0.05 0.17
## [7] 0.15 0.82 0.05 0.51 0.04
## [1] -264506.39 0.64 0.25 0.06 0.05 0.17
## [7] 0.15 0.82 0.06 0.52 0.04
## [1] -264515.52 0.64 0.25 0.06 0.05 0.18
## [7] 0.16 0.81 0.06 0.52 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -265933.53 0.55 0.26 0.16 0.02 0.13
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -264071.05 0.60 0.24 0.13 0.03 0.14
## [7] 0.11 0.88 0.05 0.51 0.04
## [1] -263961.23 0.62 0.23 0.12 0.03 0.15
## [7] 0.11 0.88 0.06 0.51 0.04
## [1] -263992.53 0.63 0.22 0.11 0.04 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264031.72 0.63 0.21 0.10 0.05 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264052.59 0.64 0.21 0.10 0.05 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264052.24 0.64 0.21 0.10 0.06 0.15
## [7] 0.13 0.86 0.08 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268327.69 0.57 0.27 0.13 0.02 0.14
## [7] 0.10 0.88 0.04 0.50 0.05
## [1] -265244.38 0.62 0.26 0.10 0.03 0.16
## [7] 0.11 0.86 0.05 0.51 0.04
## [1] -264777.32 0.63 0.25 0.08 0.03 0.17
## [7] 0.11 0.85 0.05 0.51 0.04
## [1] -264611.62 0.64 0.25 0.07 0.04 0.17
## [7] 0.12 0.84 0.06 0.51 0.04
## [1] -264544.80 0.64 0.24 0.07 0.05 0.18
## [7] 0.13 0.84 0.06 0.51 0.04
## [1] -264519.73 0.64 0.24 0.07 0.05 0.18
## [7] 0.13 0.83 0.07 0.52 0.04
## [1] -264512.51 0.64 0.24 0.06 0.05 0.18
## [7] 0.13 0.83 0.07 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -263896.17 0.53 0.28 0.17 0.02 0.13
## [7] 0.10 0.89 0.03 0.51 0.04
## [1] -262666.79 0.57 0.26 0.15 0.03 0.13
## [7] 0.11 0.88 0.04 0.51 0.04
## [1] -262764.58 0.58 0.25 0.13 0.03 0.14
## [7] 0.11 0.88 0.04 0.52 0.03
## [1] -262945.65 0.59 0.24 0.12 0.04 0.14
## [7] 0.12 0.88 0.04 0.52 0.03
## [1] -263099.52 0.59 0.24 0.12 0.05 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263205.18 0.59 0.24 0.12 0.05 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263263.73 0.59 0.24 0.12 0.06 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263283.02 0.58 0.24 0.12 0.06 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263272.14 0.58 0.24 0.12 0.07 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263239.43 0.57 0.24 0.12 0.07 0.14
## [7] 0.11 0.88 0.04 0.53 0.03
## [1] -263191.70 0.57 0.24 0.12 0.08 0.14
## [7] 0.11 0.89 0.04 0.53 0.03
## [1] -263134.21 0.56 0.24 0.12 0.08 0.13
## [7] 0.11 0.89 0.03 0.53 0.03
## [1] -263070.82 0.56 0.24 0.12 0.09 0.13
## [7] 0.11 0.89 0.03 0.54 0.03
## [1] -263004.31 0.55 0.24 0.12 0.09 0.13
## [7] 0.11 0.89 0.03 0.54 0.03
## [1] -262936.65 0.54 0.24 0.12 0.09 0.13
## [7] 0.10 0.89 0.03 0.54 0.03
## [1] -262869.21 0.54 0.24 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262802.94 0.53 0.24 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262738.49 0.53 0.25 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262676.33 0.52 0.25 0.12 0.11 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262616.73 0.52 0.25 0.12 0.11 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262559.87 0.51 0.25 0.13 0.11 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262505.87 0.51 0.25 0.13 0.12 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262454.74 0.50 0.25 0.13 0.12 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262406.49 0.50 0.25 0.13 0.12 0.12
## [7] 0.09 0.89 0.03 0.53 0.04
## [1] -262361.06 0.49 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262318.39 0.49 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262278.38 0.48 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262240.94 0.47 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262205.95 0.47 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262173.30 0.46 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262142.87 0.46 0.26 0.14 0.15 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262114.55 0.45 0.26 0.14 0.15 0.12
## [7] 0.08 0.89 0.03 0.53 0.05
## [1] -262088.22 0.45 0.26 0.14 0.15 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262063.77 0.44 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262041.10 0.44 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262020.09 0.43 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262000.64 0.43 0.26 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261982.67 0.42 0.27 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261966.07 0.42 0.27 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261950.77 0.41 0.27 0.14 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261936.67 0.41 0.27 0.15 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261923.71 0.40 0.27 0.15 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261911.80 0.40 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] -261900.89 0.39 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] -261890.90 0.38 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -262708.15 0.52 0.31 0.15 0.02 0.12
## [7] 0.10 0.89 0.04 0.51 0.04
## [1] -262094.06 0.55 0.30 0.12 0.03 0.12
## [7] 0.11 0.89 0.04 0.51 0.04
## [1] -262305.06 0.57 0.29 0.10 0.04 0.12
## [7] 0.11 0.89 0.04 0.51 0.03
## [1] -262532.42 0.58 0.29 0.09 0.04 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262689.47 0.58 0.28 0.09 0.05 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262769.54 0.57 0.28 0.09 0.06 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262784.47 0.57 0.28 0.08 0.07 0.12
## [7] 0.10 0.89 0.04 0.52 0.03
## [1] -262750.07 0.57 0.28 0.08 0.07 0.12
## [7] 0.10 0.89 0.04 0.52 0.03
## [1] -262681.12 0.56 0.28 0.08 0.08 0.11
## [7] 0.10 0.90 0.04 0.52 0.03
## [1] -262589.52 0.55 0.28 0.08 0.08 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -262483.94 0.55 0.28 0.08 0.09 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -262370.21 0.54 0.28 0.08 0.10 0.11
## [7] 0.08 0.90 0.03 0.52 0.03
## [1] -262252.07 0.54 0.28 0.08 0.10 0.11
## [7] 0.08 0.90 0.03 0.52 0.03
## [1] -262131.87 0.53 0.28 0.09 0.10 0.10
## [7] 0.08 0.90 0.03 0.52 0.04
## [1] -262011.14 0.52 0.28 0.09 0.11 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261890.93 0.52 0.28 0.09 0.11 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261772.07 0.51 0.28 0.09 0.12 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261655.24 0.51 0.28 0.09 0.12 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261541.06 0.50 0.28 0.09 0.13 0.10
## [7] 0.06 0.90 0.03 0.52 0.05
## [1] -261430.07 0.50 0.28 0.09 0.13 0.10
## [7] 0.06 0.90 0.03 0.52 0.05
## [1] -261322.75 0.50 0.28 0.09 0.14 0.09
## [7] 0.06 0.90 0.02 0.52 0.05
## [1] -261219.50 0.49 0.28 0.09 0.14 0.09
## [7] 0.06 0.90 0.02 0.52 0.05
## [1] -261120.66 0.49 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.05
## [1] -261026.50 0.48 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260937.21 0.48 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260852.92 0.47 0.28 0.09 0.16 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260773.68 0.47 0.28 0.09 0.16 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260699.51 0.46 0.28 0.09 0.17 0.09
## [7] 0.05 0.90 0.02 0.51 0.07
## [1] -260630.35 0.46 0.28 0.09 0.17 0.09
## [7] 0.05 0.90 0.02 0.51 0.07
## [1] -260566.12 0.46 0.28 0.09 0.18 0.09
## [7] 0.04 0.90 0.02 0.51 0.07
## [1] -260506.69 0.45 0.28 0.10 0.18 0.09
## [7] 0.04 0.90 0.02 0.50 0.07
## [1] -260451.91 0.45 0.27 0.10 0.18 0.08
## [7] 0.04 0.90 0.02 0.50 0.07
## [1] -260401.60 0.44 0.27 0.10 0.19 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260355.58 0.44 0.27 0.10 0.19 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260313.63 0.43 0.27 0.10 0.20 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260275.55 0.43 0.27 0.10 0.20 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260241.11 0.42 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260210.12 0.42 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260182.35 0.41 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260157.59 0.41 0.27 0.10 0.22 0.08
## [7] 0.04 0.90 0.02 0.49 0.09
## [1] -260135.65 0.40 0.27 0.10 0.22 0.08
## [7] 0.03 0.90 0.02 0.49 0.09
## [1] -260116.33 0.40 0.27 0.10 0.23 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260099.44 0.39 0.27 0.10 0.23 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260084.80 0.39 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260072.24 0.38 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260061.60 0.38 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260052.73 0.37 0.27 0.10 0.25 0.08
## [7] 0.03 0.90 0.02 0.49 0.11
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266156.99 0.55 0.23 0.20 0.02 0.14
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -264021.98 0.60 0.21 0.17 0.03 0.16
## [7] 0.11 0.88 0.04 0.52 0.04
## [1] -263767.65 0.62 0.19 0.16 0.03 0.16
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -263720.83 0.63 0.18 0.16 0.04 0.17
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -263732.49 0.63 0.17 0.15 0.04 0.17
## [7] 0.13 0.87 0.05 0.54 0.04
## [1] -263758.32 0.63 0.17 0.15 0.04 0.17
## [7] 0.13 0.87 0.06 0.54 0.04
## [1] -263781.74 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.87 0.06 0.54 0.04
## [1] -263797.15 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.86 0.06 0.54 0.04
## [1] -263803.70 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.86 0.06 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269727.89 0.59 0.24 0.15 0.02 0.16
## [7] 0.10 0.87 0.04 0.50 0.05
## [1] -265824.52 0.64 0.22 0.11 0.03 0.18
## [7] 0.10 0.86 0.05 0.51 0.05
## [1] -265105.89 0.66 0.21 0.10 0.04 0.19
## [7] 0.11 0.85 0.05 0.51 0.05
## [1] -264831.72 0.66 0.20 0.09 0.04 0.20
## [7] 0.12 0.84 0.06 0.52 0.05
## [1] -264724.35 0.67 0.20 0.09 0.05 0.20
## [7] 0.12 0.83 0.06 0.52 0.05
## [1] -264692.83 0.67 0.20 0.09 0.05 0.21
## [7] 0.13 0.82 0.06 0.52 0.05
## [1] -264695.34 0.66 0.20 0.08 0.05 0.21
## [7] 0.13 0.82 0.06 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269947.47 0.59 0.23 0.16 0.02 0.16
## [7] 0.10 0.87 0.03 0.51 0.05
## [1] -264846.57 0.63 0.20 0.14 0.03 0.17
## [7] 0.10 0.85 0.04 0.52 0.05
## [1] -263995.09 0.65 0.19 0.13 0.03 0.18
## [7] 0.11 0.84 0.04 0.53 0.05
## [1] -263712.86 0.65 0.18 0.13 0.04 0.19
## [7] 0.12 0.83 0.04 0.53 0.05
## [1] -263630.37 0.65 0.17 0.13 0.05 0.20
## [7] 0.12 0.82 0.04 0.54 0.05
## [1] -263629.81 0.65 0.17 0.13 0.05 0.20
## [7] 0.13 0.82 0.04 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269866.23 0.59 0.25 0.14 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -265124.22 0.63 0.22 0.11 0.03 0.17
## [7] 0.10 0.85 0.04 0.51 0.05
## [1] -264322.14 0.65 0.21 0.10 0.04 0.18
## [7] 0.11 0.83 0.04 0.52 0.04
## [1] -264044.04 0.65 0.20 0.10 0.04 0.19
## [7] 0.12 0.83 0.04 0.52 0.04
## [1] -263955.18 0.65 0.20 0.10 0.05 0.19
## [7] 0.12 0.82 0.04 0.53 0.04
## [1] -263947.09 0.65 0.20 0.10 0.05 0.19
## [7] 0.13 0.81 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269220.74 0.58 0.24 0.16 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -264564.15 0.62 0.22 0.13 0.03 0.16
## [7] 0.10 0.85 0.03 0.52 0.05
## [1] -263861.30 0.64 0.21 0.12 0.03 0.17
## [7] 0.11 0.84 0.04 0.52 0.04
## [1] -263650.80 0.64 0.20 0.12 0.04 0.18
## [7] 0.12 0.83 0.04 0.53 0.04
## [1] -263599.31 0.64 0.20 0.12 0.04 0.18
## [7] 0.12 0.83 0.04 0.53 0.04
## [1] -263607.13 0.64 0.19 0.12 0.05 0.18
## [7] 0.13 0.82 0.04 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269547.80 0.58 0.26 0.14 0.02 0.14
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -264858.17 0.62 0.24 0.11 0.03 0.16
## [7] 0.11 0.84 0.03 0.52 0.05
## [1] -264064.33 0.64 0.23 0.10 0.03 0.17
## [7] 0.11 0.83 0.04 0.52 0.04
## [1] -263814.50 0.64 0.22 0.10 0.04 0.17
## [7] 0.12 0.82 0.04 0.53 0.04
## [1] -263755.59 0.64 0.22 0.09 0.05 0.17
## [7] 0.13 0.81 0.04 0.53 0.04
## [1] -263772.13 0.64 0.22 0.09 0.05 0.18
## [7] 0.13 0.81 0.04 0.53 0.04
## [1] -263813.35 0.63 0.22 0.10 0.06 0.18
## [7] 0.13 0.80 0.04 0.54 0.04
## [1] -263855.78 0.62 0.22 0.10 0.06 0.18
## [7] 0.13 0.80 0.04 0.54 0.04
## [1] -263889.57 0.62 0.22 0.10 0.06 0.18
## [7] 0.14 0.80 0.04 0.54 0.04
## [1] -263911.83 0.61 0.22 0.10 0.07 0.18
## [7] 0.14 0.79 0.05 0.54 0.04
## [1] -263923.03 0.60 0.23 0.10 0.07 0.18
## [7] 0.14 0.79 0.05 0.54 0.05
## [1] -263925.03 0.59 0.23 0.11 0.07 0.19
## [7] 0.14 0.79 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259769.23 0.48 0.32 0.18 0.02 0.11
## [7] 0.09 0.90 0.03 0.51 0.04
## [1] -258980.52 0.50 0.31 0.16 0.03 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -258886.69 0.51 0.31 0.15 0.04 0.10
## [7] 0.08 0.90 0.03 0.53 0.02
## [1] -258870.28 0.51 0.30 0.14 0.05 0.10
## [7] 0.07 0.90 0.03 0.53 0.02
## [1] -258823.43 0.50 0.30 0.14 0.06 0.10
## [7] 0.06 0.91 0.03 0.53 0.02
## [1] -258740.24 0.49 0.30 0.14 0.07 0.09
## [7] 0.06 0.91 0.03 0.53 0.02
## [1] -258641.01 0.48 0.30 0.14 0.09 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258540.12 0.47 0.30 0.14 0.09 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258442.98 0.46 0.30 0.14 0.10 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258351.39 0.45 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258266.40 0.45 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258188.69 0.44 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258118.51 0.44 0.30 0.14 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258055.68 0.43 0.30 0.14 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257999.70 0.43 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257949.91 0.42 0.30 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257905.61 0.42 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257866.12 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257830.82 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257799.17 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257770.69 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257744.98 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257721.71 0.39 0.31 0.15 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257700.60 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257681.41 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257663.93 0.38 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257647.99 0.38 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257633.45 0.37 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257620.19 0.37 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257608.09 0.36 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257597.06 0.36 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257587.03 0.36 0.32 0.16 0.16 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257577.92 0.35 0.32 0.16 0.16 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259752.33 0.48 0.30 0.21 0.02 0.11
## [7] 0.09 0.90 0.03 0.52 0.04
## [1] -258793.74 0.50 0.29 0.19 0.02 0.11
## [7] 0.08 0.90 0.03 0.53 0.03
## [1] -258696.51 0.51 0.28 0.18 0.03 0.11
## [7] 0.08 0.90 0.03 0.53 0.02
## [1] -258686.29 0.51 0.27 0.17 0.04 0.10
## [7] 0.07 0.91 0.03 0.54 0.02
## [1] -258671.76 0.50 0.27 0.17 0.06 0.10
## [7] 0.06 0.91 0.03 0.54 0.02
## [1] -258638.62 0.50 0.27 0.17 0.07 0.10
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258590.02 0.49 0.27 0.17 0.08 0.10
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258529.95 0.48 0.27 0.17 0.08 0.09
## [7] 0.05 0.91 0.02 0.54 0.02
## [1] -258461.69 0.47 0.27 0.17 0.09 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258388.73 0.46 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258314.57 0.46 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258242.06 0.45 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258173.12 0.45 0.27 0.17 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258108.77 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258049.41 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -257994.98 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -257945.22 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.02 0.55 0.03
## [1] -257899.73 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257858.09 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257819.88 0.42 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257784.72 0.42 0.28 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257752.28 0.42 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257722.24 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257694.36 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257668.41 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257644.20 0.40 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257621.57 0.40 0.28 0.19 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257600.38 0.40 0.28 0.19 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257580.51 0.39 0.28 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257561.86 0.39 0.28 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257544.34 0.39 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257527.87 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257512.39 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257497.84 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257484.16 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257471.32 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.04
## [1] -257459.26 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.04
## [1] -257447.96 0.36 0.29 0.19 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] -257437.38 0.36 0.29 0.19 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] -257427.48 0.36 0.29 0.20 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259682.08 0.48 0.32 0.19 0.02 0.11
## [7] 0.09 0.90 0.03 0.52 0.04
## [1] -258562.83 0.50 0.31 0.16 0.02 0.11
## [7] 0.08 0.90 0.03 0.53 0.03
## [1] -258287.60 0.51 0.31 0.15 0.04 0.10
## [7] 0.07 0.90 0.03 0.54 0.02
## [1] -258147.95 0.50 0.30 0.15 0.05 0.10
## [7] 0.06 0.91 0.03 0.54 0.02
## [1] -258041.31 0.49 0.30 0.14 0.06 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -257953.81 0.48 0.30 0.14 0.07 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -257877.75 0.47 0.30 0.14 0.09 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257803.33 0.46 0.30 0.14 0.09 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257726.26 0.45 0.30 0.15 0.10 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257647.80 0.45 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257571.12 0.44 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257498.89 0.43 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257432.62 0.43 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257372.84 0.42 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257319.39 0.42 0.31 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257271.81 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257229.49 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257191.79 0.41 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257158.14 0.40 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257128.01 0.40 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257100.95 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257076.59 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257054.59 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257034.68 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257016.64 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257000.28 0.37 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256985.42 0.37 0.32 0.16 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256971.93 0.37 0.32 0.16 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256959.68 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256948.57 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256938.52 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256929.44 0.35 0.33 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267714.39 0.56 0.23 0.20 0.02 0.16
## [7] 0.08 0.89 0.04 0.51 0.05
## [1] -263938.90 0.59 0.21 0.17 0.02 0.17
## [7] 0.08 0.88 0.05 0.52 0.04
## [1] -263526.33 0.61 0.20 0.16 0.03 0.18
## [7] 0.08 0.87 0.05 0.53 0.04
## [1] -263411.47 0.62 0.19 0.16 0.03 0.18
## [7] 0.09 0.87 0.06 0.53 0.04
## [1] -263379.37 0.62 0.19 0.15 0.04 0.18
## [7] 0.09 0.87 0.06 0.54 0.04
## [1] -263376.50 0.62 0.18 0.15 0.04 0.18
## [7] 0.09 0.87 0.06 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -253828.02 0.42 0.34 0.22 0.01 0.08
## [7] 0.09 0.92 0.03 0.53 0.03
## [1] -252199.55 0.43 0.34 0.21 0.02 0.08
## [7] 0.07 0.93 0.03 0.54 0.02
## [1] -250701.09 0.42 0.34 0.20 0.04 0.07
## [7] 0.05 0.93 0.02 0.55 0.02
## [1] -249255.09 0.41 0.34 0.20 0.05 0.07
## [7] 0.04 0.93 0.02 0.55 0.01
## [1] -248268.42 0.39 0.34 0.20 0.07 0.06
## [7] 0.03 0.93 0.02 0.55 0.01
## [1] -247715.74 0.38 0.34 0.20 0.08 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247407.95 0.37 0.34 0.20 0.09 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247216.70 0.36 0.34 0.20 0.10 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247084.74 0.36 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -246988.48 0.35 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246916.56 0.35 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246862.17 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246820.65 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246788.64 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246763.70 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246744.05 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246728.40 0.33 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246715.78 0.33 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246705.51 0.33 0.34 0.21 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246697.05 0.33 0.34 0.21 0.13 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268311.76 0.56 0.26 0.16 0.02 0.14
## [7] 0.10 0.87 0.04 0.51 0.05
## [1] -264869.59 0.60 0.24 0.13 0.02 0.15
## [7] 0.10 0.86 0.04 0.52 0.05
## [1] -264264.43 0.62 0.23 0.12 0.03 0.16
## [7] 0.11 0.85 0.05 0.52 0.05
## [1] -264075.80 0.63 0.22 0.11 0.03 0.16
## [7] 0.11 0.84 0.05 0.53 0.05
## [1] -264033.05 0.63 0.22 0.11 0.04 0.16
## [7] 0.11 0.83 0.05 0.54 0.05
## [1] -264045.28 0.63 0.21 0.11 0.04 0.16
## [7] 0.12 0.83 0.06 0.54 0.05
## [1] -264073.40 0.63 0.21 0.11 0.04 0.16
## [7] 0.12 0.82 0.06 0.54 0.05
## [1] -264100.52 0.63 0.21 0.11 0.05 0.16
## [7] 0.12 0.82 0.06 0.54 0.05
## [1] -264120.22 0.63 0.21 0.11 0.05 0.16
## [7] 0.12 0.82 0.06 0.55 0.05
## [1] -264131.03 0.62 0.21 0.11 0.05 0.16
## [7] 0.12 0.81 0.06 0.55 0.05
## [1] -264133.60 0.62 0.21 0.11 0.05 0.16
## [7] 0.12 0.81 0.07 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -254974.48 0.43 0.34 0.22 0.01 0.09
## [7] 0.08 0.92 0.04 0.53 0.03
## [1] -252511.69 0.43 0.34 0.21 0.02 0.08
## [7] 0.06 0.93 0.03 0.54 0.02
## [1] -250890.99 0.42 0.34 0.20 0.03 0.08
## [7] 0.04 0.93 0.03 0.55 0.02
## [1] -249675.09 0.41 0.34 0.20 0.05 0.07
## [7] 0.03 0.93 0.02 0.56 0.01
## [1] -249019.66 0.40 0.34 0.20 0.07 0.07
## [7] 0.03 0.93 0.02 0.56 0.01
## [1] -248695.64 0.38 0.34 0.20 0.08 0.07
## [7] 0.02 0.93 0.02 0.56 0.01
## [1] -248505.23 0.37 0.34 0.20 0.09 0.07
## [7] 0.02 0.93 0.02 0.56 0.01
## [1] -248368.00 0.36 0.34 0.20 0.10 0.07
## [7] 0.02 0.94 0.02 0.56 0.01
## [1] -248260.60 0.36 0.34 0.20 0.10 0.07
## [7] 0.02 0.94 0.02 0.56 0.01
## [1] -248176.03 0.35 0.34 0.20 0.11 0.07
## [7] 0.02 0.94 0.02 0.56 0.02
## [1] -248110.23 0.35 0.34 0.20 0.11 0.07
## [7] 0.02 0.94 0.02 0.56 0.02
## [1] -248059.55 0.34 0.34 0.20 0.11 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -248020.73 0.34 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247991.03 0.34 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247968.26 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247950.76 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247937.26 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247926.81 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247918.69 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268423.74 0.56 0.26 0.16 0.02 0.14
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264725.62 0.60 0.24 0.14 0.02 0.16
## [7] 0.09 0.86 0.05 0.52 0.05
## [1] -264166.59 0.61 0.23 0.12 0.03 0.16
## [7] 0.10 0.85 0.05 0.52 0.05
## [1] -263987.36 0.62 0.23 0.12 0.03 0.16
## [7] 0.10 0.85 0.05 0.53 0.05
## [1] -263932.07 0.63 0.22 0.12 0.04 0.17
## [7] 0.10 0.84 0.06 0.53 0.05
## [1] -263924.51 0.63 0.22 0.12 0.04 0.17
## [7] 0.10 0.84 0.06 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269112.94 0.57 0.19 0.22 0.02 0.19
## [7] 0.07 0.90 0.04 0.50 0.05
## [1] -262769.93 0.60 0.18 0.19 0.02 0.21
## [7] 0.06 0.90 0.05 0.51 0.05
## [1] -262337.82 0.61 0.18 0.18 0.03 0.22
## [7] 0.06 0.89 0.06 0.52 0.04
## [1] -262300.57 0.61 0.18 0.18 0.04 0.22
## [7] 0.06 0.89 0.06 0.52 0.04
## [1] -262314.44 0.61 0.18 0.17 0.04 0.22
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] -262327.74 0.61 0.17 0.17 0.04 0.23
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] -262333.13 0.60 0.18 0.17 0.05 0.23
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268870.79 0.57 0.22 0.20 0.02 0.15
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264611.78 0.61 0.19 0.17 0.02 0.17
## [7] 0.09 0.86 0.04 0.52 0.05
## [1] -263880.92 0.63 0.18 0.17 0.03 0.18
## [7] 0.10 0.85 0.05 0.53 0.05
## [1] -263638.33 0.63 0.17 0.16 0.03 0.18
## [7] 0.10 0.85 0.05 0.54 0.05
## [1] -263565.74 0.63 0.17 0.16 0.04 0.18
## [7] 0.11 0.84 0.05 0.54 0.05
## [1] -263560.16 0.63 0.16 0.17 0.04 0.19
## [7] 0.11 0.84 0.05 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266085.21 0.54 0.26 0.18 0.02 0.14
## [7] 0.09 0.89 0.04 0.51 0.05
## [1] -263827.11 0.58 0.24 0.16 0.02 0.15
## [7] 0.10 0.89 0.05 0.51 0.05
## [1] -263664.02 0.59 0.23 0.14 0.03 0.15
## [7] 0.10 0.88 0.06 0.51 0.05
## [1] -263675.17 0.60 0.23 0.14 0.03 0.15
## [7] 0.11 0.88 0.06 0.52 0.04
## [1] -263708.66 0.61 0.22 0.13 0.03 0.15
## [7] 0.11 0.88 0.07 0.52 0.05
## [1] -263733.79 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.88 0.07 0.52 0.05
## [1] -263744.90 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.87 0.07 0.53 0.05
## [1] -263743.16 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.87 0.07 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267783.99 0.55 0.24 0.19 0.02 0.14
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264451.58 0.59 0.22 0.17 0.02 0.16
## [7] 0.10 0.86 0.04 0.52 0.05
## [1] -263902.03 0.61 0.20 0.16 0.03 0.16
## [7] 0.10 0.86 0.05 0.53 0.05
## [1] -263734.51 0.62 0.20 0.16 0.03 0.16
## [7] 0.11 0.85 0.05 0.53 0.05
## [1] -263692.89 0.62 0.19 0.15 0.03 0.17
## [7] 0.11 0.85 0.05 0.54 0.05
## [1] -263697.11 0.62 0.19 0.16 0.04 0.17
## [7] 0.11 0.84 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267731.20 0.56 0.23 0.19 0.02 0.15
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -264741.01 0.61 0.21 0.16 0.03 0.17
## [7] 0.11 0.87 0.04 0.51 0.05
## [1] -264280.40 0.63 0.19 0.15 0.03 0.18
## [7] 0.12 0.86 0.05 0.51 0.05
## [1] -264141.67 0.64 0.18 0.15 0.03 0.19
## [7] 0.13 0.86 0.05 0.52 0.05
## [1] -264103.36 0.64 0.18 0.14 0.04 0.19
## [7] 0.13 0.85 0.05 0.52 0.05
## [1] -264100.96 0.64 0.18 0.14 0.04 0.20
## [7] 0.14 0.85 0.05 0.52 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269373.79 0.57 0.23 0.18 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -264821.04 0.61 0.21 0.15 0.02 0.18
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -264141.75 0.63 0.20 0.14 0.03 0.19
## [7] 0.10 0.85 0.04 0.52 0.05
## [1] -263917.19 0.63 0.20 0.14 0.03 0.19
## [7] 0.10 0.84 0.04 0.52 0.05
## [1] -263834.91 0.64 0.19 0.14 0.04 0.20
## [7] 0.11 0.84 0.05 0.52 0.05
## [1] -263809.12 0.63 0.19 0.14 0.04 0.20
## [7] 0.11 0.84 0.05 0.53 0.05
## [1] -263807.02 0.63 0.19 0.14 0.04 0.21
## [7] 0.11 0.83 0.05 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269824.44 0.58 0.22 0.18 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -264469.04 0.61 0.20 0.16 0.02 0.18
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -263727.89 0.63 0.19 0.15 0.03 0.19
## [7] 0.09 0.85 0.04 0.52 0.05
## [1] -263495.11 0.63 0.19 0.15 0.03 0.20
## [7] 0.09 0.84 0.04 0.53 0.05
## [1] -263416.64 0.63 0.18 0.15 0.04 0.21
## [7] 0.09 0.84 0.04 0.53 0.05
## [1] -263398.92 0.63 0.18 0.15 0.04 0.21
## [7] 0.10 0.84 0.05 0.54 0.05
## [1] -263406.91 0.63 0.18 0.15 0.04 0.21
## [7] 0.10 0.83 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266204.55 0.54 0.29 0.15 0.02 0.13
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -263950.82 0.58 0.28 0.12 0.03 0.14
## [7] 0.10 0.87 0.04 0.51 0.04
## [1] -263705.08 0.60 0.27 0.10 0.03 0.14
## [7] 0.11 0.86 0.05 0.52 0.04
## [1] -263667.70 0.61 0.26 0.10 0.04 0.14
## [7] 0.11 0.86 0.05 0.52 0.04
## [1] -263677.68 0.61 0.26 0.09 0.04 0.15
## [7] 0.11 0.85 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267788.65 0.56 0.25 0.17 0.02 0.14
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -264614.76 0.60 0.23 0.14 0.02 0.16
## [7] 0.10 0.86 0.04 0.51 0.05
## [1] -264115.96 0.61 0.22 0.13 0.03 0.16
## [7] 0.11 0.86 0.05 0.52 0.05
## [1] -263956.11 0.62 0.22 0.13 0.03 0.17
## [7] 0.11 0.85 0.05 0.53 0.05
## [1] -263908.95 0.63 0.21 0.13 0.04 0.17
## [7] 0.12 0.85 0.05 0.53 0.05
## [1] -263905.77 0.63 0.21 0.13 0.04 0.17
## [7] 0.12 0.84 0.06 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -265331.09 0.54 0.19 0.25 0.02 0.15
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -263295.51 0.58 0.16 0.23 0.02 0.16
## [7] 0.12 0.88 0.04 0.52 0.04
## [1] -262972.47 0.60 0.14 0.23 0.03 0.17
## [7] 0.13 0.88 0.05 0.53 0.04
## [1] -262887.34 0.61 0.13 0.23 0.03 0.18
## [7] 0.14 0.87 0.05 0.54 0.04
## [1] -262885.31 0.61 0.12 0.23 0.04 0.19
## [7] 0.15 0.87 0.06 0.54 0.04
ggplot(sampleinfo_organoid_notfetal, aes(as.numeric(as.character(passage.or.rescope.no_numeric)), thresholded_prior_I))+
geom_point(size=2,shape=21,color="black",aes(fill=as.factor(passage.or.rescope.no_numeric)))+xlab("Passage")+
ylab("Intermediate Peak Prior")+theme_bw()+theme(axis.title = element_text(size=12))+
#geom_text(aes(label=count, vjust=vjust, hjust=hjust), color="grey40", size=3)+
scale_x_continuous(breaks=c(1,2,3,4,6,7,8,2,4,10,11,14,16))+ scale_fill_manual(values=pass_col,name="Passage\nNumber", guide=F)
ggsave(here("figs","MTAB4957_mixture_model_prior_I.pdf"), width=3, height=2)
sampleinfo_organoid_notfetal$thresholded_prior10<-F
sampleinfo_organoid_notfetal$thresholded_prior10[which(sampleinfo_organoid_notfetal$thresholded_prior_I>0.10)]<-T
percent_passing<-round((tapply(sampleinfo_organoid_notfetal$thresholded_prior10, sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric, sum)/tapply(sampleinfo_organoid_notfetal$array.id, sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric, length))*100,2)
passed_num<-tapply(sampleinfo_organoid_notfetal$thresholded_prior10, sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric, sum)
org_numer<-tapply(sampleinfo_organoid_notfetal$array.id, sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric, length)
df<-data.frame(passage=names(percent_passing), passing=percent_passing, pro_passing=percent_passing/100, count=org_numer, passed_num=passed_num)
df$passage.factor <- factor(df$passage, levels = c(11,9,8,6,4,3,2,1))
df<-cbind(df,(binom.confint(df$passed_num, df$count, method="exact", conf.level=0.95)))
df$upper<-df$upper*100
df$lower<-df$lower*100
ggplot(df, aes(as.numeric(as.character(passage)), passing))+
geom_errorbar(aes(ymin=lower, ymax=upper), colour="grey70", width=.25)+
geom_line(color="grey20")+geom_point(size=1.25,shape=21,color="black",aes(fill=passage.factor))+xlab("Passage")+
ylab("Samples with Trimodal\nDistribution (%)")+theme_bw()+theme(axis.title = element_text(size=10))+
scale_x_continuous(breaks=c(1,2,3,4,6,7,8,2,4,10,11,14,16))+ scale_fill_manual(values=pass_col,name="Passage\nNumber", guide=F)
ggsave(here("figs","MTAB4957_mixture_model_prior_I_threshold.pdf"), width=3, height=2)
## plot all samples
plts_paired<-lapply(1:nrow(sampleinfo_organoid_notfetal), function(x){
passage<-paste("passage: ",sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric[x],"\nIndividual: ", sampleinfo_organoid_notfetal$Characteristics.individual.[x],"\nPrior I: " ,round(sampleinfo_organoid_notfetal$thresholded_prior_I[x],2), sep="")
converted<-as.numeric(round(MTAB4957_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
draw_fit_params_gg(converted, counts, res,passage)
})
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -270103.38 0.60 0.23 0.15 0.02 0.16
## [7] 0.10 0.87 0.04 0.51 0.05
## [1] -265615.03 0.64 0.20 0.12 0.03 0.18
## [7] 0.11 0.85 0.04 0.51 0.05
## [1] -264789.93 0.66 0.19 0.11 0.04 0.20
## [7] 0.11 0.84 0.04 0.52 0.05
## [1] -264484.65 0.67 0.18 0.10 0.04 0.21
## [7] 0.12 0.83 0.05 0.52 0.05
## [1] -264372.38 0.67 0.18 0.10 0.05 0.22
## [7] 0.13 0.83 0.05 0.52 0.05
## [1] -264345.26 0.67 0.18 0.10 0.05 0.22
## [7] 0.13 0.82 0.05 0.53 0.05
## [1] -264354.33 0.66 0.18 0.10 0.06 0.23
## [7] 0.13 0.82 0.05 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267948.50 0.57 0.28 0.12 0.02 0.14
## [7] 0.11 0.87 0.04 0.50 0.05
## [1] -265300.54 0.62 0.26 0.09 0.03 0.15
## [7] 0.12 0.85 0.04 0.51 0.04
## [1] -264779.32 0.63 0.25 0.08 0.04 0.16
## [7] 0.13 0.84 0.05 0.51 0.04
## [1] -264588.26 0.64 0.25 0.07 0.04 0.17
## [7] 0.14 0.83 0.05 0.51 0.04
## [1] -264520.21 0.64 0.25 0.07 0.05 0.17
## [7] 0.15 0.82 0.05 0.51 0.04
## [1] -264506.39 0.64 0.25 0.06 0.05 0.17
## [7] 0.15 0.82 0.06 0.52 0.04
## [1] -264515.52 0.64 0.25 0.06 0.05 0.18
## [7] 0.16 0.81 0.06 0.52 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -265933.53 0.55 0.26 0.16 0.02 0.13
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -264071.05 0.60 0.24 0.13 0.03 0.14
## [7] 0.11 0.88 0.05 0.51 0.04
## [1] -263961.23 0.62 0.23 0.12 0.03 0.15
## [7] 0.11 0.88 0.06 0.51 0.04
## [1] -263992.53 0.63 0.22 0.11 0.04 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264031.72 0.63 0.21 0.10 0.05 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264052.59 0.64 0.21 0.10 0.05 0.15
## [7] 0.12 0.87 0.07 0.52 0.04
## [1] -264052.24 0.64 0.21 0.10 0.06 0.15
## [7] 0.13 0.86 0.08 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268327.69 0.57 0.27 0.13 0.02 0.14
## [7] 0.10 0.88 0.04 0.50 0.05
## [1] -265244.38 0.62 0.26 0.10 0.03 0.16
## [7] 0.11 0.86 0.05 0.51 0.04
## [1] -264777.32 0.63 0.25 0.08 0.03 0.17
## [7] 0.11 0.85 0.05 0.51 0.04
## [1] -264611.62 0.64 0.25 0.07 0.04 0.17
## [7] 0.12 0.84 0.06 0.51 0.04
## [1] -264544.80 0.64 0.24 0.07 0.05 0.18
## [7] 0.13 0.84 0.06 0.51 0.04
## [1] -264519.73 0.64 0.24 0.07 0.05 0.18
## [7] 0.13 0.83 0.07 0.52 0.04
## [1] -264512.51 0.64 0.24 0.06 0.05 0.18
## [7] 0.13 0.83 0.07 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -263896.17 0.53 0.28 0.17 0.02 0.13
## [7] 0.10 0.89 0.03 0.51 0.04
## [1] -262666.79 0.57 0.26 0.15 0.03 0.13
## [7] 0.11 0.88 0.04 0.51 0.04
## [1] -262764.58 0.58 0.25 0.13 0.03 0.14
## [7] 0.11 0.88 0.04 0.52 0.03
## [1] -262945.65 0.59 0.24 0.12 0.04 0.14
## [7] 0.12 0.88 0.04 0.52 0.03
## [1] -263099.52 0.59 0.24 0.12 0.05 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263205.18 0.59 0.24 0.12 0.05 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263263.73 0.59 0.24 0.12 0.06 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263283.02 0.58 0.24 0.12 0.06 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263272.14 0.58 0.24 0.12 0.07 0.14
## [7] 0.12 0.88 0.04 0.53 0.03
## [1] -263239.43 0.57 0.24 0.12 0.07 0.14
## [7] 0.11 0.88 0.04 0.53 0.03
## [1] -263191.70 0.57 0.24 0.12 0.08 0.14
## [7] 0.11 0.89 0.04 0.53 0.03
## [1] -263134.21 0.56 0.24 0.12 0.08 0.13
## [7] 0.11 0.89 0.03 0.53 0.03
## [1] -263070.82 0.56 0.24 0.12 0.09 0.13
## [7] 0.11 0.89 0.03 0.54 0.03
## [1] -263004.31 0.55 0.24 0.12 0.09 0.13
## [7] 0.11 0.89 0.03 0.54 0.03
## [1] -262936.65 0.54 0.24 0.12 0.09 0.13
## [7] 0.10 0.89 0.03 0.54 0.03
## [1] -262869.21 0.54 0.24 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262802.94 0.53 0.24 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262738.49 0.53 0.25 0.12 0.10 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262676.33 0.52 0.25 0.12 0.11 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262616.73 0.52 0.25 0.12 0.11 0.13
## [7] 0.10 0.89 0.03 0.54 0.04
## [1] -262559.87 0.51 0.25 0.13 0.11 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262505.87 0.51 0.25 0.13 0.12 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262454.74 0.50 0.25 0.13 0.12 0.13
## [7] 0.09 0.89 0.03 0.54 0.04
## [1] -262406.49 0.50 0.25 0.13 0.12 0.12
## [7] 0.09 0.89 0.03 0.53 0.04
## [1] -262361.06 0.49 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262318.39 0.49 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262278.38 0.48 0.25 0.13 0.13 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262240.94 0.47 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262205.95 0.47 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262173.30 0.46 0.26 0.13 0.14 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262142.87 0.46 0.26 0.14 0.15 0.12
## [7] 0.09 0.89 0.03 0.53 0.05
## [1] -262114.55 0.45 0.26 0.14 0.15 0.12
## [7] 0.08 0.89 0.03 0.53 0.05
## [1] -262088.22 0.45 0.26 0.14 0.15 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262063.77 0.44 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262041.10 0.44 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262020.09 0.43 0.26 0.14 0.16 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -262000.64 0.43 0.26 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261982.67 0.42 0.27 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261966.07 0.42 0.27 0.14 0.17 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261950.77 0.41 0.27 0.14 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261936.67 0.41 0.27 0.15 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261923.71 0.40 0.27 0.15 0.18 0.12
## [7] 0.08 0.89 0.03 0.53 0.06
## [1] -261911.80 0.40 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] -261900.89 0.39 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] -261890.90 0.38 0.27 0.15 0.19 0.12
## [7] 0.08 0.89 0.03 0.53 0.07
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -262708.15 0.52 0.31 0.15 0.02 0.12
## [7] 0.10 0.89 0.04 0.51 0.04
## [1] -262094.06 0.55 0.30 0.12 0.03 0.12
## [7] 0.11 0.89 0.04 0.51 0.04
## [1] -262305.06 0.57 0.29 0.10 0.04 0.12
## [7] 0.11 0.89 0.04 0.51 0.03
## [1] -262532.42 0.58 0.29 0.09 0.04 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262689.47 0.58 0.28 0.09 0.05 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262769.54 0.57 0.28 0.09 0.06 0.12
## [7] 0.11 0.89 0.04 0.52 0.03
## [1] -262784.47 0.57 0.28 0.08 0.07 0.12
## [7] 0.10 0.89 0.04 0.52 0.03
## [1] -262750.07 0.57 0.28 0.08 0.07 0.12
## [7] 0.10 0.89 0.04 0.52 0.03
## [1] -262681.12 0.56 0.28 0.08 0.08 0.11
## [7] 0.10 0.90 0.04 0.52 0.03
## [1] -262589.52 0.55 0.28 0.08 0.08 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -262483.94 0.55 0.28 0.08 0.09 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -262370.21 0.54 0.28 0.08 0.10 0.11
## [7] 0.08 0.90 0.03 0.52 0.03
## [1] -262252.07 0.54 0.28 0.08 0.10 0.11
## [7] 0.08 0.90 0.03 0.52 0.03
## [1] -262131.87 0.53 0.28 0.09 0.10 0.10
## [7] 0.08 0.90 0.03 0.52 0.04
## [1] -262011.14 0.52 0.28 0.09 0.11 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261890.93 0.52 0.28 0.09 0.11 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261772.07 0.51 0.28 0.09 0.12 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261655.24 0.51 0.28 0.09 0.12 0.10
## [7] 0.07 0.90 0.03 0.52 0.04
## [1] -261541.06 0.50 0.28 0.09 0.13 0.10
## [7] 0.06 0.90 0.03 0.52 0.05
## [1] -261430.07 0.50 0.28 0.09 0.13 0.10
## [7] 0.06 0.90 0.03 0.52 0.05
## [1] -261322.75 0.50 0.28 0.09 0.14 0.09
## [7] 0.06 0.90 0.02 0.52 0.05
## [1] -261219.50 0.49 0.28 0.09 0.14 0.09
## [7] 0.06 0.90 0.02 0.52 0.05
## [1] -261120.66 0.49 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.05
## [1] -261026.50 0.48 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260937.21 0.48 0.28 0.09 0.15 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260852.92 0.47 0.28 0.09 0.16 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260773.68 0.47 0.28 0.09 0.16 0.09
## [7] 0.05 0.90 0.02 0.51 0.06
## [1] -260699.51 0.46 0.28 0.09 0.17 0.09
## [7] 0.05 0.90 0.02 0.51 0.07
## [1] -260630.35 0.46 0.28 0.09 0.17 0.09
## [7] 0.05 0.90 0.02 0.51 0.07
## [1] -260566.12 0.46 0.28 0.09 0.18 0.09
## [7] 0.04 0.90 0.02 0.51 0.07
## [1] -260506.69 0.45 0.28 0.10 0.18 0.09
## [7] 0.04 0.90 0.02 0.50 0.07
## [1] -260451.91 0.45 0.27 0.10 0.18 0.08
## [7] 0.04 0.90 0.02 0.50 0.07
## [1] -260401.60 0.44 0.27 0.10 0.19 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260355.58 0.44 0.27 0.10 0.19 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260313.63 0.43 0.27 0.10 0.20 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260275.55 0.43 0.27 0.10 0.20 0.08
## [7] 0.04 0.90 0.02 0.50 0.08
## [1] -260241.11 0.42 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260210.12 0.42 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260182.35 0.41 0.27 0.10 0.21 0.08
## [7] 0.04 0.90 0.02 0.50 0.09
## [1] -260157.59 0.41 0.27 0.10 0.22 0.08
## [7] 0.04 0.90 0.02 0.49 0.09
## [1] -260135.65 0.40 0.27 0.10 0.22 0.08
## [7] 0.03 0.90 0.02 0.49 0.09
## [1] -260116.33 0.40 0.27 0.10 0.23 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260099.44 0.39 0.27 0.10 0.23 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260084.80 0.39 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260072.24 0.38 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260061.60 0.38 0.27 0.10 0.24 0.08
## [7] 0.03 0.90 0.02 0.49 0.10
## [1] -260052.73 0.37 0.27 0.10 0.25 0.08
## [7] 0.03 0.90 0.02 0.49 0.11
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266156.99 0.55 0.23 0.20 0.02 0.14
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -264021.98 0.60 0.21 0.17 0.03 0.16
## [7] 0.11 0.88 0.04 0.52 0.04
## [1] -263767.65 0.62 0.19 0.16 0.03 0.16
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -263720.83 0.63 0.18 0.16 0.04 0.17
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -263732.49 0.63 0.17 0.15 0.04 0.17
## [7] 0.13 0.87 0.05 0.54 0.04
## [1] -263758.32 0.63 0.17 0.15 0.04 0.17
## [7] 0.13 0.87 0.06 0.54 0.04
## [1] -263781.74 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.87 0.06 0.54 0.04
## [1] -263797.15 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.86 0.06 0.54 0.04
## [1] -263803.70 0.63 0.17 0.15 0.05 0.17
## [7] 0.14 0.86 0.06 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269727.89 0.59 0.24 0.15 0.02 0.16
## [7] 0.10 0.87 0.04 0.50 0.05
## [1] -265824.52 0.64 0.22 0.11 0.03 0.18
## [7] 0.10 0.86 0.05 0.51 0.05
## [1] -265105.89 0.66 0.21 0.10 0.04 0.19
## [7] 0.11 0.85 0.05 0.51 0.05
## [1] -264831.72 0.66 0.20 0.09 0.04 0.20
## [7] 0.12 0.84 0.06 0.52 0.05
## [1] -264724.35 0.67 0.20 0.09 0.05 0.20
## [7] 0.12 0.83 0.06 0.52 0.05
## [1] -264692.83 0.67 0.20 0.09 0.05 0.21
## [7] 0.13 0.82 0.06 0.52 0.05
## [1] -264695.34 0.66 0.20 0.08 0.05 0.21
## [7] 0.13 0.82 0.06 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269947.47 0.59 0.23 0.16 0.02 0.16
## [7] 0.10 0.87 0.03 0.51 0.05
## [1] -264846.57 0.63 0.20 0.14 0.03 0.17
## [7] 0.10 0.85 0.04 0.52 0.05
## [1] -263995.09 0.65 0.19 0.13 0.03 0.18
## [7] 0.11 0.84 0.04 0.53 0.05
## [1] -263712.86 0.65 0.18 0.13 0.04 0.19
## [7] 0.12 0.83 0.04 0.53 0.05
## [1] -263630.37 0.65 0.17 0.13 0.05 0.20
## [7] 0.12 0.82 0.04 0.54 0.05
## [1] -263629.81 0.65 0.17 0.13 0.05 0.20
## [7] 0.13 0.82 0.04 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269866.23 0.59 0.25 0.14 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -265124.22 0.63 0.22 0.11 0.03 0.17
## [7] 0.10 0.85 0.04 0.51 0.05
## [1] -264322.14 0.65 0.21 0.10 0.04 0.18
## [7] 0.11 0.83 0.04 0.52 0.04
## [1] -264044.04 0.65 0.20 0.10 0.04 0.19
## [7] 0.12 0.83 0.04 0.52 0.04
## [1] -263955.18 0.65 0.20 0.10 0.05 0.19
## [7] 0.12 0.82 0.04 0.53 0.04
## [1] -263947.09 0.65 0.20 0.10 0.05 0.19
## [7] 0.13 0.81 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269220.74 0.58 0.24 0.16 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -264564.15 0.62 0.22 0.13 0.03 0.16
## [7] 0.10 0.85 0.03 0.52 0.05
## [1] -263861.30 0.64 0.21 0.12 0.03 0.17
## [7] 0.11 0.84 0.04 0.52 0.04
## [1] -263650.80 0.64 0.20 0.12 0.04 0.18
## [7] 0.12 0.83 0.04 0.53 0.04
## [1] -263599.31 0.64 0.20 0.12 0.04 0.18
## [7] 0.12 0.83 0.04 0.53 0.04
## [1] -263607.13 0.64 0.19 0.12 0.05 0.18
## [7] 0.13 0.82 0.04 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269547.80 0.58 0.26 0.14 0.02 0.14
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -264858.17 0.62 0.24 0.11 0.03 0.16
## [7] 0.11 0.84 0.03 0.52 0.05
## [1] -264064.33 0.64 0.23 0.10 0.03 0.17
## [7] 0.11 0.83 0.04 0.52 0.04
## [1] -263814.50 0.64 0.22 0.10 0.04 0.17
## [7] 0.12 0.82 0.04 0.53 0.04
## [1] -263755.59 0.64 0.22 0.09 0.05 0.17
## [7] 0.13 0.81 0.04 0.53 0.04
## [1] -263772.13 0.64 0.22 0.09 0.05 0.18
## [7] 0.13 0.81 0.04 0.53 0.04
## [1] -263813.35 0.63 0.22 0.10 0.06 0.18
## [7] 0.13 0.80 0.04 0.54 0.04
## [1] -263855.78 0.62 0.22 0.10 0.06 0.18
## [7] 0.13 0.80 0.04 0.54 0.04
## [1] -263889.57 0.62 0.22 0.10 0.06 0.18
## [7] 0.14 0.80 0.04 0.54 0.04
## [1] -263911.83 0.61 0.22 0.10 0.07 0.18
## [7] 0.14 0.79 0.05 0.54 0.04
## [1] -263923.03 0.60 0.23 0.10 0.07 0.18
## [7] 0.14 0.79 0.05 0.54 0.05
## [1] -263925.03 0.59 0.23 0.11 0.07 0.19
## [7] 0.14 0.79 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259769.23 0.48 0.32 0.18 0.02 0.11
## [7] 0.09 0.90 0.03 0.51 0.04
## [1] -258980.52 0.50 0.31 0.16 0.03 0.11
## [7] 0.09 0.90 0.03 0.52 0.03
## [1] -258886.69 0.51 0.31 0.15 0.04 0.10
## [7] 0.08 0.90 0.03 0.53 0.02
## [1] -258870.28 0.51 0.30 0.14 0.05 0.10
## [7] 0.07 0.90 0.03 0.53 0.02
## [1] -258823.43 0.50 0.30 0.14 0.06 0.10
## [7] 0.06 0.91 0.03 0.53 0.02
## [1] -258740.24 0.49 0.30 0.14 0.07 0.09
## [7] 0.06 0.91 0.03 0.53 0.02
## [1] -258641.01 0.48 0.30 0.14 0.09 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258540.12 0.47 0.30 0.14 0.09 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258442.98 0.46 0.30 0.14 0.10 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258351.39 0.45 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258266.40 0.45 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258188.69 0.44 0.30 0.14 0.11 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258118.51 0.44 0.30 0.14 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -258055.68 0.43 0.30 0.14 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257999.70 0.43 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257949.91 0.42 0.30 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257905.61 0.42 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257866.12 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257830.82 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257799.17 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257770.69 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257744.98 0.40 0.31 0.15 0.14 0.09
## [7] 0.04 0.91 0.03 0.53 0.03
## [1] -257721.71 0.39 0.31 0.15 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257700.60 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257681.41 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.90 0.03 0.53 0.03
## [1] -257663.93 0.38 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257647.99 0.38 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257633.45 0.37 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257620.19 0.37 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257608.09 0.36 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257597.06 0.36 0.32 0.16 0.15 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257587.03 0.36 0.32 0.16 0.16 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] -257577.92 0.35 0.32 0.16 0.16 0.09
## [7] 0.05 0.90 0.03 0.53 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259752.33 0.48 0.30 0.21 0.02 0.11
## [7] 0.09 0.90 0.03 0.52 0.04
## [1] -258793.74 0.50 0.29 0.19 0.02 0.11
## [7] 0.08 0.90 0.03 0.53 0.03
## [1] -258696.51 0.51 0.28 0.18 0.03 0.11
## [7] 0.08 0.90 0.03 0.53 0.02
## [1] -258686.29 0.51 0.27 0.17 0.04 0.10
## [7] 0.07 0.91 0.03 0.54 0.02
## [1] -258671.76 0.50 0.27 0.17 0.06 0.10
## [7] 0.06 0.91 0.03 0.54 0.02
## [1] -258638.62 0.50 0.27 0.17 0.07 0.10
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258590.02 0.49 0.27 0.17 0.08 0.10
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -258529.95 0.48 0.27 0.17 0.08 0.09
## [7] 0.05 0.91 0.02 0.54 0.02
## [1] -258461.69 0.47 0.27 0.17 0.09 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258388.73 0.46 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258314.57 0.46 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258242.06 0.45 0.27 0.17 0.10 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258173.12 0.45 0.27 0.17 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258108.77 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -258049.41 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -257994.98 0.44 0.27 0.18 0.11 0.09
## [7] 0.04 0.91 0.02 0.55 0.02
## [1] -257945.22 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.02 0.55 0.03
## [1] -257899.73 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257858.09 0.43 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257819.88 0.42 0.27 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257784.72 0.42 0.28 0.18 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257752.28 0.42 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257722.24 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257694.36 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257668.41 0.41 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257644.20 0.40 0.28 0.18 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257621.57 0.40 0.28 0.19 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257600.38 0.40 0.28 0.19 0.13 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257580.51 0.39 0.28 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257561.86 0.39 0.28 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257544.34 0.39 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257527.87 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257512.39 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257497.84 0.38 0.29 0.19 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257484.16 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257471.32 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.04
## [1] -257459.26 0.37 0.29 0.19 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.04
## [1] -257447.96 0.36 0.29 0.19 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] -257437.38 0.36 0.29 0.19 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] -257427.48 0.36 0.29 0.20 0.15 0.10
## [7] 0.05 0.91 0.03 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -259682.08 0.48 0.32 0.19 0.02 0.11
## [7] 0.09 0.90 0.03 0.52 0.04
## [1] -258562.83 0.50 0.31 0.16 0.02 0.11
## [7] 0.08 0.90 0.03 0.53 0.03
## [1] -258287.60 0.51 0.31 0.15 0.04 0.10
## [7] 0.07 0.90 0.03 0.54 0.02
## [1] -258147.95 0.50 0.30 0.15 0.05 0.10
## [7] 0.06 0.91 0.03 0.54 0.02
## [1] -258041.31 0.49 0.30 0.14 0.06 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -257953.81 0.48 0.30 0.14 0.07 0.09
## [7] 0.05 0.91 0.03 0.54 0.02
## [1] -257877.75 0.47 0.30 0.14 0.09 0.09
## [7] 0.04 0.91 0.03 0.54 0.02
## [1] -257803.33 0.46 0.30 0.14 0.09 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257726.26 0.45 0.30 0.15 0.10 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257647.80 0.45 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257571.12 0.44 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257498.89 0.43 0.30 0.15 0.11 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257432.62 0.43 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257372.84 0.42 0.30 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257319.39 0.42 0.31 0.15 0.12 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257271.81 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257229.49 0.41 0.31 0.15 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.02
## [1] -257191.79 0.41 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257158.14 0.40 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257128.01 0.40 0.31 0.16 0.13 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257100.95 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257076.59 0.39 0.31 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257054.59 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257034.68 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.55 0.03
## [1] -257016.64 0.38 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -257000.28 0.37 0.32 0.16 0.14 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256985.42 0.37 0.32 0.16 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256971.93 0.37 0.32 0.16 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256959.68 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256948.57 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256938.52 0.36 0.32 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] -256929.44 0.35 0.33 0.17 0.15 0.09
## [7] 0.04 0.91 0.03 0.54 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267714.39 0.56 0.23 0.20 0.02 0.16
## [7] 0.08 0.89 0.04 0.51 0.05
## [1] -263938.90 0.59 0.21 0.17 0.02 0.17
## [7] 0.08 0.88 0.05 0.52 0.04
## [1] -263526.33 0.61 0.20 0.16 0.03 0.18
## [7] 0.08 0.87 0.05 0.53 0.04
## [1] -263411.47 0.62 0.19 0.16 0.03 0.18
## [7] 0.09 0.87 0.06 0.53 0.04
## [1] -263379.37 0.62 0.19 0.15 0.04 0.18
## [7] 0.09 0.87 0.06 0.54 0.04
## [1] -263376.50 0.62 0.18 0.15 0.04 0.18
## [7] 0.09 0.87 0.06 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -253828.02 0.42 0.34 0.22 0.01 0.08
## [7] 0.09 0.92 0.03 0.53 0.03
## [1] -252199.55 0.43 0.34 0.21 0.02 0.08
## [7] 0.07 0.93 0.03 0.54 0.02
## [1] -250701.09 0.42 0.34 0.20 0.04 0.07
## [7] 0.05 0.93 0.02 0.55 0.02
## [1] -249255.09 0.41 0.34 0.20 0.05 0.07
## [7] 0.04 0.93 0.02 0.55 0.01
## [1] -248268.42 0.39 0.34 0.20 0.07 0.06
## [7] 0.03 0.93 0.02 0.55 0.01
## [1] -247715.74 0.38 0.34 0.20 0.08 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247407.95 0.37 0.34 0.20 0.09 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247216.70 0.36 0.34 0.20 0.10 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -247084.74 0.36 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.55 0.01
## [1] -246988.48 0.35 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246916.56 0.35 0.34 0.20 0.11 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246862.17 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246820.65 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246788.64 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246763.70 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246744.05 0.34 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246728.40 0.33 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246715.78 0.33 0.34 0.20 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246705.51 0.33 0.34 0.21 0.12 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -246697.05 0.33 0.34 0.21 0.13 0.06
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268311.76 0.56 0.26 0.16 0.02 0.14
## [7] 0.10 0.87 0.04 0.51 0.05
## [1] -264869.59 0.60 0.24 0.13 0.02 0.15
## [7] 0.10 0.86 0.04 0.52 0.05
## [1] -264264.43 0.62 0.23 0.12 0.03 0.16
## [7] 0.11 0.85 0.05 0.52 0.05
## [1] -264075.80 0.63 0.22 0.11 0.03 0.16
## [7] 0.11 0.84 0.05 0.53 0.05
## [1] -264033.05 0.63 0.22 0.11 0.04 0.16
## [7] 0.11 0.83 0.05 0.54 0.05
## [1] -264045.28 0.63 0.21 0.11 0.04 0.16
## [7] 0.12 0.83 0.06 0.54 0.05
## [1] -264073.40 0.63 0.21 0.11 0.04 0.16
## [7] 0.12 0.82 0.06 0.54 0.05
## [1] -264100.52 0.63 0.21 0.11 0.05 0.16
## [7] 0.12 0.82 0.06 0.54 0.05
## [1] -264120.22 0.63 0.21 0.11 0.05 0.16
## [7] 0.12 0.82 0.06 0.55 0.05
## [1] -264131.03 0.62 0.21 0.11 0.05 0.16
## [7] 0.12 0.81 0.06 0.55 0.05
## [1] -264133.60 0.62 0.21 0.11 0.05 0.16
## [7] 0.12 0.81 0.07 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -254974.48 0.43 0.34 0.22 0.01 0.09
## [7] 0.08 0.92 0.04 0.53 0.03
## [1] -252511.69 0.43 0.34 0.21 0.02 0.08
## [7] 0.06 0.93 0.03 0.54 0.02
## [1] -250890.99 0.42 0.34 0.20 0.03 0.08
## [7] 0.04 0.93 0.03 0.55 0.02
## [1] -249675.09 0.41 0.34 0.20 0.05 0.07
## [7] 0.03 0.93 0.02 0.56 0.01
## [1] -249019.66 0.40 0.34 0.20 0.07 0.07
## [7] 0.03 0.93 0.02 0.56 0.01
## [1] -248695.64 0.38 0.34 0.20 0.08 0.07
## [7] 0.02 0.93 0.02 0.56 0.01
## [1] -248505.23 0.37 0.34 0.20 0.09 0.07
## [7] 0.02 0.93 0.02 0.56 0.01
## [1] -248368.00 0.36 0.34 0.20 0.10 0.07
## [7] 0.02 0.94 0.02 0.56 0.01
## [1] -248260.60 0.36 0.34 0.20 0.10 0.07
## [7] 0.02 0.94 0.02 0.56 0.01
## [1] -248176.03 0.35 0.34 0.20 0.11 0.07
## [7] 0.02 0.94 0.02 0.56 0.02
## [1] -248110.23 0.35 0.34 0.20 0.11 0.07
## [7] 0.02 0.94 0.02 0.56 0.02
## [1] -248059.55 0.34 0.34 0.20 0.11 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -248020.73 0.34 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247991.03 0.34 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247968.26 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247950.76 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247937.26 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247926.81 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] -247918.69 0.33 0.34 0.21 0.12 0.07
## [7] 0.02 0.93 0.02 0.56 0.02
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268423.74 0.56 0.26 0.16 0.02 0.14
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264725.62 0.60 0.24 0.14 0.02 0.16
## [7] 0.09 0.86 0.05 0.52 0.05
## [1] -264166.59 0.61 0.23 0.12 0.03 0.16
## [7] 0.10 0.85 0.05 0.52 0.05
## [1] -263987.36 0.62 0.23 0.12 0.03 0.16
## [7] 0.10 0.85 0.05 0.53 0.05
## [1] -263932.07 0.63 0.22 0.12 0.04 0.17
## [7] 0.10 0.84 0.06 0.53 0.05
## [1] -263924.51 0.63 0.22 0.12 0.04 0.17
## [7] 0.10 0.84 0.06 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269112.94 0.57 0.19 0.22 0.02 0.19
## [7] 0.07 0.90 0.04 0.50 0.05
## [1] -262769.93 0.60 0.18 0.19 0.02 0.21
## [7] 0.06 0.90 0.05 0.51 0.05
## [1] -262337.82 0.61 0.18 0.18 0.03 0.22
## [7] 0.06 0.89 0.06 0.52 0.04
## [1] -262300.57 0.61 0.18 0.18 0.04 0.22
## [7] 0.06 0.89 0.06 0.52 0.04
## [1] -262314.44 0.61 0.18 0.17 0.04 0.22
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] -262327.74 0.61 0.17 0.17 0.04 0.23
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] -262333.13 0.60 0.18 0.17 0.05 0.23
## [7] 0.06 0.89 0.07 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -268870.79 0.57 0.22 0.20 0.02 0.15
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264611.78 0.61 0.19 0.17 0.02 0.17
## [7] 0.09 0.86 0.04 0.52 0.05
## [1] -263880.92 0.63 0.18 0.17 0.03 0.18
## [7] 0.10 0.85 0.05 0.53 0.05
## [1] -263638.33 0.63 0.17 0.16 0.03 0.18
## [7] 0.10 0.85 0.05 0.54 0.05
## [1] -263565.74 0.63 0.17 0.16 0.04 0.18
## [7] 0.11 0.84 0.05 0.54 0.05
## [1] -263560.16 0.63 0.16 0.17 0.04 0.19
## [7] 0.11 0.84 0.05 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266085.21 0.54 0.26 0.18 0.02 0.14
## [7] 0.09 0.89 0.04 0.51 0.05
## [1] -263827.11 0.58 0.24 0.16 0.02 0.15
## [7] 0.10 0.89 0.05 0.51 0.05
## [1] -263664.02 0.59 0.23 0.14 0.03 0.15
## [7] 0.10 0.88 0.06 0.51 0.05
## [1] -263675.17 0.60 0.23 0.14 0.03 0.15
## [7] 0.11 0.88 0.06 0.52 0.04
## [1] -263708.66 0.61 0.22 0.13 0.03 0.15
## [7] 0.11 0.88 0.07 0.52 0.05
## [1] -263733.79 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.88 0.07 0.52 0.05
## [1] -263744.90 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.87 0.07 0.53 0.05
## [1] -263743.16 0.61 0.22 0.13 0.04 0.15
## [7] 0.11 0.87 0.07 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267783.99 0.55 0.24 0.19 0.02 0.14
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -264451.58 0.59 0.22 0.17 0.02 0.16
## [7] 0.10 0.86 0.04 0.52 0.05
## [1] -263902.03 0.61 0.20 0.16 0.03 0.16
## [7] 0.10 0.86 0.05 0.53 0.05
## [1] -263734.51 0.62 0.20 0.16 0.03 0.16
## [7] 0.11 0.85 0.05 0.53 0.05
## [1] -263692.89 0.62 0.19 0.15 0.03 0.17
## [7] 0.11 0.85 0.05 0.54 0.05
## [1] -263697.11 0.62 0.19 0.16 0.04 0.17
## [7] 0.11 0.84 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267731.20 0.56 0.23 0.19 0.02 0.15
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -264741.01 0.61 0.21 0.16 0.03 0.17
## [7] 0.11 0.87 0.04 0.51 0.05
## [1] -264280.40 0.63 0.19 0.15 0.03 0.18
## [7] 0.12 0.86 0.05 0.51 0.05
## [1] -264141.67 0.64 0.18 0.15 0.03 0.19
## [7] 0.13 0.86 0.05 0.52 0.05
## [1] -264103.36 0.64 0.18 0.14 0.04 0.19
## [7] 0.13 0.85 0.05 0.52 0.05
## [1] -264100.96 0.64 0.18 0.14 0.04 0.20
## [7] 0.14 0.85 0.05 0.52 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269373.79 0.57 0.23 0.18 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -264821.04 0.61 0.21 0.15 0.02 0.18
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -264141.75 0.63 0.20 0.14 0.03 0.19
## [7] 0.10 0.85 0.04 0.52 0.05
## [1] -263917.19 0.63 0.20 0.14 0.03 0.19
## [7] 0.10 0.84 0.04 0.52 0.05
## [1] -263834.91 0.64 0.19 0.14 0.04 0.20
## [7] 0.11 0.84 0.05 0.52 0.05
## [1] -263809.12 0.63 0.19 0.14 0.04 0.20
## [7] 0.11 0.84 0.05 0.53 0.05
## [1] -263807.02 0.63 0.19 0.14 0.04 0.21
## [7] 0.11 0.83 0.05 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -269824.44 0.58 0.22 0.18 0.02 0.16
## [7] 0.09 0.87 0.03 0.51 0.05
## [1] -264469.04 0.61 0.20 0.16 0.02 0.18
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -263727.89 0.63 0.19 0.15 0.03 0.19
## [7] 0.09 0.85 0.04 0.52 0.05
## [1] -263495.11 0.63 0.19 0.15 0.03 0.20
## [7] 0.09 0.84 0.04 0.53 0.05
## [1] -263416.64 0.63 0.18 0.15 0.04 0.21
## [7] 0.09 0.84 0.04 0.53 0.05
## [1] -263398.92 0.63 0.18 0.15 0.04 0.21
## [7] 0.10 0.84 0.05 0.54 0.05
## [1] -263406.91 0.63 0.18 0.15 0.04 0.21
## [7] 0.10 0.83 0.05 0.54 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -266204.55 0.54 0.29 0.15 0.02 0.13
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -263950.82 0.58 0.28 0.12 0.03 0.14
## [7] 0.10 0.87 0.04 0.51 0.04
## [1] -263705.08 0.60 0.27 0.10 0.03 0.14
## [7] 0.11 0.86 0.05 0.52 0.04
## [1] -263667.70 0.61 0.26 0.10 0.04 0.14
## [7] 0.11 0.86 0.05 0.52 0.04
## [1] -263677.68 0.61 0.26 0.09 0.04 0.15
## [7] 0.11 0.85 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -267788.65 0.56 0.25 0.17 0.02 0.14
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -264614.76 0.60 0.23 0.14 0.02 0.16
## [7] 0.10 0.86 0.04 0.51 0.05
## [1] -264115.96 0.61 0.22 0.13 0.03 0.16
## [7] 0.11 0.86 0.05 0.52 0.05
## [1] -263956.11 0.62 0.22 0.13 0.03 0.17
## [7] 0.11 0.85 0.05 0.53 0.05
## [1] -263908.95 0.63 0.21 0.13 0.04 0.17
## [7] 0.12 0.85 0.05 0.53 0.05
## [1] -263905.77 0.63 0.21 0.13 0.04 0.17
## [7] 0.12 0.84 0.06 0.53 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -265331.09 0.54 0.19 0.25 0.02 0.15
## [7] 0.10 0.89 0.04 0.51 0.05
## [1] -263295.51 0.58 0.16 0.23 0.02 0.16
## [7] 0.12 0.88 0.04 0.52 0.04
## [1] -262972.47 0.60 0.14 0.23 0.03 0.17
## [7] 0.13 0.88 0.05 0.53 0.04
## [1] -262887.34 0.61 0.13 0.23 0.03 0.18
## [7] 0.14 0.87 0.05 0.54 0.04
## [1] -262885.31 0.61 0.12 0.23 0.04 0.19
## [7] 0.15 0.87 0.06 0.54 0.04
plts_paired_order<-plts_paired[order(sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric)]
pdf(here("figs","MTAB4957_organoids_thresholding_all_samples.pdf"))
plts_paired_order
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
##
## [[7]]
##
## [[8]]
##
## [[9]]
##
## [[10]]
##
## [[11]]
##
## [[12]]
##
## [[13]]
##
## [[14]]
##
## [[15]]
##
## [[16]]
##
## [[17]]
##
## [[18]]
##
## [[19]]
##
## [[20]]
##
## [[21]]
##
## [[22]]
##
## [[23]]
##
## [[24]]
##
## [[25]]
##
## [[26]]
##
## [[27]]
##
## [[28]]
##
## [[29]]
##
## [[30]]
dev.off()
## png
## 2
sampleinfo_organoid_fetal<-sampleinfo_organoid[which(sampleinfo_organoid$Characteristics.biosource.type.=="organoid" & sampleinfo_organoid$Characteristics.developmental.stage.=="fetal stage"),]
sampleinfo_organoid_fetal<-sampleinfo_organoid_fetal[-grep("KO", sampleinfo_organoid_fetal$condition),]
MTAB_organoid_beta_fetal<-MTAB_organoid_beta[,which(colnames(MTAB_organoid_beta)%in%sampleinfo_organoid_fetal$Assay.Name)]
identical(colnames(MTAB_organoid_beta_fetal),sampleinfo_organoid_fetal$Assay.Name)
## [1] TRUE
# ' ### PCA organoids
pca_res <- prcomp(t(MTAB_organoid_beta_fetal))
Loadings<-as.data.frame(pca_res$x)
vars <- pca_res$sdev^2
Importance<-vars/sum(vars)
meta_categorical <- sampleinfo_organoid_fetal[, c(4,8,13,17,18)] # input column numbers in meta that contain categorical variables
meta_continuous <- sampleinfo_organoid_fetal[, c(9,21)] # input column numbers in meta that contain continuous variables
colnames(meta_categorical) <- c("Individual", "Sample Site","Sex","Block","Sentrix ID")
colnames(meta_continuous) <- c("Age", "Passage")
meta_continuous$Age<-as.numeric(meta_continuous$Age)
meta_categorical$Block<-as.factor(meta_categorical$Block)
ord<-1:length(c(colnames(meta_categorical),colnames(meta_continuous)))
PCs_to_view<-10
suppressWarnings(heat_scree_plot(Loadings, Importance, 2.5, 2.7))
## PC vs PC plot
Loadings$Assay.Name<-rownames(Loadings)
Loadings_meta<-merge(Loadings, sampleinfo_organoid_fetal, by="Assay.Name")
Sample Site
ggplot(Loadings_meta, aes(PC1, PC2, fill=Characteristics.sampling.site.))+geom_point(shape=21,size=3, color="black")+theme_bw()+
xlab("PC1 (20%)")+ylab("PC2 (13%)")+th+theme(axis.text = element_text(size=12),
axis.title = element_text(size=14),
plot.margin = margin(1, 0.1, 1, 1, "cm"))
pc_plt<-ggplot(Loadings_meta, aes(PC1, PC2, fill=as.factor(passage.or.rescope.no_numeric)))+geom_line(aes(PC1,PC2, group=sample_ID), color="lightgrey")+#, color=sampling.time.point
geom_point(shape=21,size=3)+#
theme_bw()+xlab("PC1 (36%)")+ylab("PC1 (14%)")+th+theme(axis.text = element_text(size=12),axis.title = element_text(size=14))+
scale_fill_manual(values=c(colorRampPalette(brewer.pal(11, "Spectral"))(11), "#544791","#4a3e80", "#40366f","#221d3c"),name="Passage\nNumber")+scale_color_manual(values=c("black","white","black"))
legend<-ggplot(sampleinfo_organoid_fetal, aes(as.factor(-passage.or.rescope.no_numeric), fill=as.factor(passage.or.rescope.no_numeric)))+geom_bar(color="black")+
theme_bw()+theme(legend.position = "none", axis.text.y = element_blank(),
axis.title.y = element_blank(),
axis.ticks.y = element_blank(),
legend.title=element_text(size=10),
legend.text=element_text(size=8))+
coord_flip()+
scale_fill_manual(values=c(colorRampPalette(brewer.pal(11, "Spectral"))(11), "#544791","#4a3e80", "#40366f","#221d3c"),name="Passage\nNumber")+th
r <- ggplot() + theme_void()
grid.arrange(pc_plt,arrangeGrob(r,legend,r, heights=c(0.6,1.25,0.4)), ncol=2, widths=c(7,1))
Variation<-function(x) {quantile(x, c(0.9), na.rm=T)[[1]]-quantile(x, c(0.1), na.rm=T)[[1]]}
Mval<-function(beta) log2(beta/(1-beta))
MTAB4957_mval= apply(MTAB_organoid_beta_fetal, 1, Mval) # need mvalues for combat
MTAB4957_mval = as.data.frame(MTAB4957_mval)
MTAB4957_mval = t(MTAB4957_mval)
ref_range_dnam<-sapply(1:nrow(MTAB4957_mval), function(x) Variation(MTAB4957_mval[x,]))
dim(MTAB4957_beta_VeryVariable<-MTAB_organoid_beta_fetal[which(ref_range_dnam>=2.75),])# 28418
## [1] 28418 26
## Beta distribution plot
Beta_melted<- melt(MTAB4957_beta_VeryVariable)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,sampleinfo_organoid_fetal, by.x="ID", by.y="Assay.Name")
Beta_Plot$passage.or.rescope.no_numeric.factor <- factor(Beta_Plot$passage.or.rescope.no_numeric, levels = c(23,21,14,12,9,7,6,5,3,2,1))
ggplot(Beta_Plot, aes(Beta,color=passage.or.rescope.no_numeric.factor))+
geom_density(size=1)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=pass_col, name="Passage\nNumber")+th+theme(legend.text = element_text(size=7),
legend.title = element_text(size=10),
legend.key.size = unit(0.7,"line"))
To view the beta distributions we will also include a line for the 11 primary fetal samples to compare each passage to primary
identical(colnames(organoid_fetal_primary),sampleinfo_fetal_primary$Assay.Name)
## [1] TRUE
MTAB4957_mval= apply(organoid_fetal_primary, 1, Mval) # need mvalues for combat
MTAB4957_mval = as.data.frame(MTAB4957_mval)
MTAB4957_mval = t(MTAB4957_mval)
ref_range_dnam_fetal<-sapply(1:nrow(MTAB4957_mval), function(x) Variation(MTAB4957_mval[x,]))
dim(organoid_fetal_primary_VeryVariable<-organoid_fetal_primary[rev(order(ref_range_dnam_fetal)),])
## [1] 409528 11
dim(organoid_fetal_primary_VeryVariable<-organoid_fetal_primary_VeryVariable[1:28418 ,])# same number as MTAB organoid varible
## [1] 28418 11
Beta_melted_MTAB_primary<- melt(organoid_fetal_primary_VeryVariable)
Beta_Plot_MTAB_primary<-Beta_melted_MTAB_primary[which(!(is.na(Beta_melted_MTAB_primary$value))),]
colnames(Beta_Plot_MTAB_primary)<-c("CpG","ID","Beta")
Beta_Plot_MTAB_primary<-merge(Beta_Plot_MTAB_primary,sampleinfo_fetal_primary, by.x="ID", by.y="Assay.Name")
Beta_plot_primary<-Beta_Plot_MTAB_primary[,c(1:3)]
Beta_plot_primary$passage.or.rescope.no_numeric<-0
Beta_Plot<-Beta_Plot[,c(1:3,23)]
Beta_Plot_combined<-rbind(Beta_plot_primary,Beta_Plot)
Beta_Plot_combined$passage.or.rescope.no_numeric.factor <- factor(Beta_Plot_combined$passage.or.rescope.no_numeric, levels = c(23,21,14,12,9,7,6,5,3,2,1,0))
ggplot(Beta_Plot_combined, aes(Beta,color=as.factor(passage.or.rescope.no_numeric.factor)))+
geom_density(size=1)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values=pass_col, name="Passage\nNumber")+th+theme(legend.text = element_text(size=7),
legend.title = element_text(size=10),
legend.key.size = unit(0.7,"line"))
ggsave(here("figs","MTAB4957_beta_fetal_with_primary.pdf"),width = 3.75, height = 2.5)
ggsave(here("figs/jpeg","MTAB4957_beta_fetal_with_primary.jpeg"), w=5, h=3)
sampleinfo_organoid_fetal$sample_ID<-paste(sampleinfo_organoid_fetal$Characteristics.individual., sampleinfo_organoid_fetal$Characteristics.sampling.site.)
sampleinfo_organoid_paired<-sampleinfo_organoid_fetal[which(sampleinfo_organoid_fetal$sample_ID%in%sampleinfo_organoid_fetal$sample_ID[duplicated(sampleinfo_organoid_fetal$sample_ID)]),]
MTAB4957.organoid_paired<-do.call(rbind,lapply(1:length(unique(sampleinfo_organoid_paired$sample_ID)), function(x){
sample<-unique(sampleinfo_organoid_paired$sample_ID)[x]
samp<-sampleinfo_organoid_paired[sampleinfo_organoid_paired$sample_ID==sample,]
samp<-samp[order(samp$passage.or.rescope.no_numeric),]
samp$hilo<-as.factor(samp$passage.or.rescope.no_numeric)
if(length(levels(samp$hilo))==2){levels(samp$hilo)<-c("lower","higher")}else{
if(length(levels(samp$hilo))==3){levels(samp$hilo)<-c("lower","higher","highest")}else{
if(length(levels(samp$hilo))==4){levels(samp$hilo)<-c("lowest","lower","higher","highest")}else{samp$hilo<-NA}
}
}
samp
}))
MTAB4957.organoid_paired<-MTAB4957.organoid_paired[which(!is.na(MTAB4957.organoid_paired$hilo)),]
MTAB4957.organoid_paired$hilo<-factor(MTAB4957.organoid_paired$hilo, c("lowest","lower","higher","highest"))
identical(colnames(MTAB4957_beta_VeryVariable), sampleinfo_organoid_fetal$Assay.Name)
## [1] TRUE
MTAB4957_beta_VeryVariable_paird<-MTAB4957_beta_VeryVariable[,which(sampleinfo_organoid_fetal$sample_ID%in%MTAB4957.organoid_paired$sample_ID)]
Beta_melted<- melt(MTAB4957_beta_VeryVariable_paird)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,MTAB4957.organoid_paired, by.x="ID", by.y="Assay.Name")
labels<-as.data.frame(tapply(MTAB4957.organoid_paired$passage.or.rescope.no_numeric, MTAB4957.organoid_paired$sample_ID, function(x) paste(x, collapse=", ")))
colnames(labels)<-"passge"
labels$sample_ID<-rownames(labels)
ggplot()+
geom_density(aes(Beta,color=hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
scale_color_manual(values = c ("#9ecae1","#4292c6", "#225ea8", "#081d58"), name="Relative\nPassage\nLevel within\nPatient")+facet_wrap(~sample_ID, nrow=2)+
geom_text(aes(0.75, 2.75, label=passge), data=labels, color="grey20")+th+theme(strip.text = element_text(size = 10),
axis.text=element_text(size=4),
panel.spacing = unit(0.7, "lines"))+
scale_x_continuous(breaks = c(0,0.5,1))
ggsave(here("figs","MTAB4957_beta_paired_fetal.pdf"),w=6, height = 3.75)
ggsave(here("figs/jpeg","MTAB4957_beta_paired_fetal.jpeg"), w=6, height = 3.75)
sampleinfo_organoid_fetal$thresholded_prior_I<-sapply(1:nrow(sampleinfo_organoid_fetal), function(x){
passage<-sampleinfo_organoid_fetal$passage.or.rescope.no_numeric[x]
converted<-as.numeric(round(MTAB4957_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
res$prior_I
})
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157952.80 0.56 0.28 0.14 0.02 0.14
## [7] 0.10 0.89 0.04 0.50 0.04
## [1] -156833.59 0.60 0.27 0.11 0.03 0.15
## [7] 0.11 0.88 0.05 0.50 0.04
## [1] -156790.71 0.61 0.26 0.09 0.04 0.16
## [7] 0.12 0.88 0.06 0.50 0.04
## [1] -156840.30 0.62 0.26 0.08 0.04 0.16
## [7] 0.13 0.87 0.06 0.50 0.04
## [1] -156896.56 0.62 0.25 0.07 0.05 0.17
## [7] 0.13 0.87 0.06 0.51 0.04
## [1] -156941.22 0.62 0.25 0.07 0.05 0.17
## [7] 0.14 0.87 0.07 0.51 0.03
## [1] -156971.46 0.62 0.25 0.07 0.06 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] -156989.01 0.62 0.25 0.07 0.06 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] -156996.69 0.62 0.25 0.06 0.07 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159957.90 0.58 0.16 0.24 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -156245.96 0.62 0.12 0.24 0.03 0.19
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155479.65 0.63 0.10 0.24 0.03 0.21
## [7] 0.12 0.84 0.03 0.55 0.05
## [1] -155229.53 0.62 0.09 0.25 0.04 0.23
## [7] 0.13 0.83 0.04 0.56 0.05
## [1] -155159.03 0.62 0.08 0.26 0.04 0.24
## [7] 0.13 0.83 0.04 0.56 0.04
## [1] -155158.76 0.61 0.08 0.26 0.05 0.25
## [7] 0.14 0.83 0.04 0.57 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -156851.65 0.52 0.33 0.14 0.02 0.13
## [7] 0.10 0.90 0.04 0.49 0.04
## [1] -155883.29 0.54 0.33 0.11 0.02 0.14
## [7] 0.10 0.90 0.05 0.49 0.04
## [1] -155955.77 0.55 0.33 0.09 0.03 0.14
## [7] 0.11 0.90 0.06 0.49 0.04
## [1] -156103.00 0.55 0.33 0.09 0.03 0.14
## [7] 0.11 0.90 0.06 0.49 0.04
## [1] -156234.08 0.55 0.33 0.08 0.04 0.15
## [7] 0.11 0.90 0.06 0.48 0.04
## [1] -156336.91 0.55 0.33 0.08 0.04 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156414.40 0.55 0.33 0.08 0.04 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156471.91 0.55 0.33 0.08 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156514.21 0.55 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156544.96 0.54 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156566.80 0.54 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.04 0.48 0.04
## [1] -156581.56 0.54 0.33 0.07 0.06 0.15
## [7] 0.12 0.91 0.04 0.48 0.04
## [1] -156590.50 0.53 0.33 0.07 0.06 0.15
## [7] 0.12 0.92 0.04 0.48 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -155944.91 0.46 0.43 0.10 0.01 0.11
## [7] 0.08 0.89 0.04 0.48 0.05
## [1] -154340.82 0.44 0.47 0.07 0.01 0.12
## [7] 0.07 0.90 0.05 0.47 0.05
## [1] -154158.94 0.44 0.49 0.06 0.02 0.12
## [7] 0.08 0.90 0.05 0.46 0.04
## [1] -154209.89 0.43 0.50 0.05 0.02 0.12
## [7] 0.08 0.90 0.05 0.46 0.04
## [1] -154316.43 0.43 0.50 0.05 0.02 0.12
## [7] 0.08 0.90 0.04 0.46 0.04
## [1] -154428.61 0.42 0.51 0.05 0.02 0.13
## [7] 0.08 0.90 0.04 0.45 0.04
## [1] -154529.96 0.42 0.51 0.05 0.02 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154615.48 0.42 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154684.35 0.41 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154737.29 0.41 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154775.57 0.41 0.52 0.05 0.03 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154800.67 0.40 0.52 0.05 0.03 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154814.12 0.40 0.52 0.05 0.04 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154817.44 0.40 0.52 0.05 0.04 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -156833.58 0.51 0.39 0.09 0.02 0.12
## [7] 0.09 0.88 0.04 0.49 0.04
## [1] -155662.25 0.51 0.41 0.05 0.02 0.13
## [7] 0.09 0.88 0.05 0.48 0.04
## [1] -155583.43 0.51 0.42 0.04 0.03 0.13
## [7] 0.10 0.87 0.05 0.47 0.04
## [1] -155650.18 0.51 0.43 0.03 0.03 0.14
## [7] 0.10 0.87 0.06 0.47 0.04
## [1] -155738.30 0.50 0.44 0.03 0.04 0.14
## [7] 0.11 0.87 0.06 0.47 0.03
## [1] -155815.07 0.49 0.44 0.02 0.04 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155871.96 0.49 0.45 0.02 0.05 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155908.99 0.48 0.45 0.02 0.05 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155929.26 0.47 0.45 0.02 0.06 0.14
## [7] 0.12 0.87 0.06 0.46 0.03
## [1] -155936.55 0.47 0.45 0.02 0.06 0.14
## [7] 0.12 0.87 0.06 0.46 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157509.21 0.54 0.25 0.19 0.02 0.13
## [7] 0.11 0.88 0.04 0.51 0.05
## [1] -156447.22 0.59 0.22 0.17 0.03 0.14
## [7] 0.12 0.87 0.04 0.52 0.04
## [1] -156309.10 0.61 0.21 0.16 0.03 0.14
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -156309.49 0.62 0.20 0.15 0.04 0.14
## [7] 0.13 0.86 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158735.16 0.57 0.29 0.11 0.02 0.13
## [7] 0.11 0.87 0.04 0.50 0.05
## [1] -157318.31 0.62 0.28 0.08 0.03 0.15
## [7] 0.12 0.86 0.05 0.51 0.04
## [1] -157020.94 0.63 0.27 0.06 0.04 0.15
## [7] 0.13 0.84 0.06 0.51 0.04
## [1] -156896.01 0.64 0.27 0.05 0.04 0.16
## [7] 0.14 0.83 0.07 0.51 0.04
## [1] -156839.73 0.64 0.26 0.05 0.05 0.16
## [7] 0.14 0.81 0.07 0.51 0.04
## [1] -156818.76 0.63 0.26 0.04 0.06 0.17
## [7] 0.15 0.80 0.07 0.51 0.04
## [1] -156816.96 0.63 0.26 0.04 0.06 0.17
## [7] 0.15 0.79 0.07 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160911.83 0.60 0.22 0.16 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -157068.71 0.64 0.19 0.14 0.03 0.17
## [7] 0.11 0.83 0.03 0.53 0.05
## [1] -156304.49 0.66 0.17 0.14 0.03 0.18
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -156080.52 0.66 0.16 0.14 0.04 0.19
## [7] 0.12 0.81 0.03 0.54 0.05
## [1] -156045.71 0.65 0.16 0.14 0.05 0.19
## [7] 0.13 0.80 0.03 0.55 0.05
## [1] -156076.03 0.65 0.16 0.14 0.05 0.20
## [7] 0.13 0.80 0.04 0.55 0.05
## [1] -156120.64 0.64 0.16 0.15 0.05 0.20
## [7] 0.13 0.79 0.04 0.56 0.05
## [1] -156159.66 0.63 0.16 0.15 0.06 0.20
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156187.17 0.62 0.16 0.15 0.06 0.21
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156203.21 0.61 0.16 0.16 0.06 0.21
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156209.91 0.60 0.17 0.16 0.07 0.21
## [7] 0.14 0.78 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -161638.23 0.62 0.19 0.16 0.02 0.17
## [7] 0.09 0.85 0.03 0.51 0.05
## [1] -157151.06 0.67 0.16 0.14 0.03 0.20
## [7] 0.10 0.83 0.03 0.53 0.05
## [1] -156228.56 0.68 0.14 0.14 0.04 0.21
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -155932.47 0.68 0.14 0.14 0.05 0.23
## [7] 0.11 0.81 0.03 0.54 0.05
## [1] -155865.39 0.67 0.13 0.14 0.05 0.24
## [7] 0.12 0.80 0.03 0.55 0.04
## [1] -155884.50 0.66 0.13 0.15 0.06 0.25
## [7] 0.12 0.79 0.04 0.55 0.04
## [1] -155928.35 0.65 0.13 0.15 0.07 0.25
## [7] 0.12 0.79 0.04 0.56 0.04
## [1] -155970.79 0.64 0.13 0.16 0.07 0.26
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156002.60 0.63 0.14 0.16 0.07 0.26
## [7] 0.13 0.78 0.04 0.56 0.04
## [1] -156022.41 0.62 0.14 0.16 0.08 0.26
## [7] 0.13 0.78 0.04 0.56 0.05
## [1] -156032.00 0.61 0.14 0.17 0.08 0.26
## [7] 0.13 0.78 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159328.07 0.58 0.22 0.18 0.02 0.15
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -157270.96 0.63 0.19 0.16 0.03 0.16
## [7] 0.11 0.86 0.05 0.53 0.05
## [1] -156822.75 0.65 0.17 0.15 0.03 0.17
## [7] 0.12 0.85 0.05 0.53 0.05
## [1] -156667.50 0.66 0.16 0.15 0.04 0.18
## [7] 0.13 0.84 0.06 0.54 0.05
## [1] -156628.51 0.66 0.15 0.15 0.04 0.18
## [7] 0.14 0.83 0.06 0.55 0.05
## [1] -156636.20 0.66 0.15 0.15 0.05 0.19
## [7] 0.14 0.83 0.06 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159121.75 0.57 0.27 0.13 0.02 0.14
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -157287.07 0.62 0.25 0.10 0.03 0.15
## [7] 0.10 0.86 0.05 0.52 0.04
## [1] -156927.53 0.64 0.24 0.09 0.03 0.15
## [7] 0.11 0.84 0.06 0.52 0.04
## [1] -156795.47 0.65 0.23 0.08 0.04 0.16
## [7] 0.12 0.83 0.06 0.53 0.04
## [1] -156752.57 0.65 0.23 0.08 0.05 0.16
## [7] 0.12 0.82 0.07 0.53 0.04
## [1] -156748.57 0.65 0.23 0.07 0.05 0.16
## [7] 0.12 0.81 0.07 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158970.73 0.57 0.17 0.24 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155944.77 0.60 0.14 0.24 0.02 0.18
## [7] 0.10 0.86 0.03 0.53 0.05
## [1] -155446.62 0.61 0.12 0.24 0.03 0.20
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155283.74 0.61 0.11 0.24 0.03 0.21
## [7] 0.12 0.85 0.04 0.55 0.04
## [1] -155234.20 0.61 0.11 0.24 0.04 0.21
## [7] 0.13 0.84 0.04 0.56 0.04
## [1] -155231.43 0.61 0.10 0.25 0.04 0.22
## [7] 0.13 0.84 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160493.51 0.60 0.20 0.18 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156915.39 0.64 0.16 0.17 0.03 0.18
## [7] 0.11 0.84 0.03 0.53 0.05
## [1] -156233.18 0.66 0.14 0.16 0.04 0.20
## [7] 0.12 0.83 0.03 0.54 0.04
## [1] -156012.04 0.66 0.14 0.16 0.04 0.21
## [7] 0.12 0.82 0.04 0.54 0.04
## [1] -155955.34 0.66 0.13 0.17 0.05 0.22
## [7] 0.13 0.82 0.04 0.55 0.04
## [1] -155961.94 0.65 0.13 0.17 0.05 0.22
## [7] 0.13 0.81 0.04 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157985.66 0.55 0.15 0.29 0.02 0.17
## [7] 0.10 0.88 0.03 0.52 0.05
## [1] -155299.24 0.57 0.11 0.29 0.02 0.19
## [7] 0.11 0.87 0.03 0.53 0.05
## [1] -154836.67 0.58 0.10 0.30 0.03 0.21
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -154674.82 0.58 0.09 0.30 0.03 0.23
## [7] 0.12 0.86 0.04 0.55 0.05
## [1] -154618.80 0.58 0.08 0.31 0.04 0.24
## [7] 0.13 0.85 0.04 0.55 0.05
## [1] -154608.82 0.57 0.08 0.31 0.04 0.25
## [7] 0.14 0.85 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160561.43 0.60 0.20 0.18 0.02 0.16
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -156977.58 0.64 0.17 0.17 0.03 0.19
## [7] 0.10 0.85 0.03 0.52 0.05
## [1] -156307.57 0.65 0.15 0.16 0.03 0.20
## [7] 0.11 0.83 0.04 0.53 0.05
## [1] -156095.62 0.66 0.14 0.16 0.04 0.21
## [7] 0.12 0.82 0.04 0.54 0.05
## [1] -156041.74 0.65 0.14 0.16 0.04 0.22
## [7] 0.12 0.82 0.04 0.55 0.05
## [1] -156046.58 0.65 0.13 0.17 0.05 0.22
## [7] 0.13 0.81 0.04 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158513.30 0.55 0.18 0.25 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155730.90 0.59 0.15 0.24 0.02 0.17
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155309.77 0.60 0.13 0.24 0.03 0.19
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -155174.71 0.60 0.12 0.25 0.03 0.19
## [7] 0.12 0.85 0.03 0.55 0.05
## [1] -155134.73 0.60 0.12 0.25 0.04 0.20
## [7] 0.13 0.85 0.04 0.55 0.05
## [1] -155134.08 0.60 0.11 0.25 0.04 0.21
## [7] 0.13 0.85 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158305.37 0.55 0.16 0.27 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155475.57 0.58 0.12 0.27 0.02 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155024.67 0.59 0.11 0.27 0.03 0.20
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -154871.25 0.59 0.10 0.27 0.03 0.22
## [7] 0.13 0.85 0.03 0.54 0.05
## [1] -154818.39 0.59 0.09 0.28 0.04 0.23
## [7] 0.14 0.85 0.04 0.55 0.05
## [1] -154808.34 0.59 0.09 0.28 0.04 0.24
## [7] 0.15 0.85 0.04 0.55 0.05
## [1] -154816.04 0.58 0.09 0.28 0.05 0.24
## [7] 0.15 0.85 0.04 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159623.23 0.58 0.17 0.23 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -156433.23 0.62 0.13 0.22 0.03 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155803.37 0.63 0.12 0.22 0.03 0.21
## [7] 0.12 0.85 0.04 0.54 0.05
## [1] -155575.47 0.64 0.11 0.22 0.04 0.22
## [7] 0.12 0.84 0.04 0.55 0.05
## [1] -155500.97 0.63 0.10 0.22 0.04 0.24
## [7] 0.13 0.84 0.04 0.56 0.05
## [1] -155492.92 0.63 0.10 0.23 0.05 0.25
## [7] 0.13 0.83 0.05 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158766.69 0.56 0.16 0.26 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155655.89 0.59 0.12 0.26 0.02 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155129.24 0.60 0.10 0.26 0.03 0.21
## [7] 0.12 0.85 0.03 0.54 0.05
## [1] -154945.49 0.60 0.10 0.27 0.04 0.23
## [7] 0.13 0.85 0.03 0.55 0.05
## [1] -154883.58 0.60 0.09 0.27 0.04 0.24
## [7] 0.14 0.85 0.04 0.55 0.05
## [1] -154874.84 0.59 0.09 0.27 0.04 0.25
## [7] 0.14 0.84 0.04 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160347.69 0.59 0.18 0.21 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156640.87 0.63 0.14 0.20 0.03 0.18
## [7] 0.11 0.84 0.03 0.53 0.05
## [1] -155891.20 0.64 0.13 0.21 0.03 0.20
## [7] 0.12 0.83 0.03 0.54 0.05
## [1] -155664.02 0.64 0.12 0.21 0.04 0.21
## [7] 0.13 0.83 0.03 0.55 0.05
## [1] -155610.24 0.64 0.11 0.21 0.04 0.22
## [7] 0.14 0.82 0.04 0.55 0.05
## [1] -155616.55 0.63 0.11 0.22 0.04 0.22
## [7] 0.14 0.82 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160298.78 0.59 0.18 0.22 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156360.09 0.62 0.14 0.21 0.03 0.18
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155596.90 0.63 0.12 0.22 0.03 0.19
## [7] 0.11 0.83 0.03 0.55 0.05
## [1] -155368.14 0.63 0.11 0.22 0.04 0.20
## [7] 0.12 0.83 0.04 0.56 0.05
## [1] -155322.88 0.63 0.10 0.23 0.04 0.21
## [7] 0.13 0.82 0.04 0.57 0.04
## [1] -155342.87 0.62 0.10 0.23 0.05 0.21
## [7] 0.13 0.82 0.04 0.57 0.04
## [1] -155380.85 0.61 0.10 0.24 0.05 0.22
## [7] 0.13 0.82 0.04 0.58 0.04
## [1] -155418.05 0.60 0.10 0.24 0.05 0.22
## [7] 0.14 0.81 0.04 0.58 0.04
## [1] -155448.12 0.60 0.10 0.25 0.06 0.22
## [7] 0.14 0.81 0.04 0.58 0.04
## [1] -155470.00 0.59 0.10 0.25 0.06 0.22
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] -155484.68 0.58 0.10 0.25 0.06 0.23
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] -155493.69 0.57 0.11 0.26 0.06 0.23
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160906.11 0.60 0.21 0.17 0.02 0.16
## [7] 0.09 0.86 0.04 0.52 0.05
## [1] -157285.13 0.65 0.18 0.15 0.03 0.18
## [7] 0.10 0.84 0.04 0.53 0.05
## [1] -156526.19 0.66 0.16 0.14 0.03 0.19
## [7] 0.10 0.83 0.04 0.54 0.05
## [1] -156276.29 0.67 0.15 0.14 0.04 0.20
## [7] 0.11 0.82 0.04 0.55 0.05
## [1] -156222.17 0.66 0.15 0.14 0.05 0.21
## [7] 0.11 0.81 0.04 0.55 0.05
## [1] -156243.48 0.66 0.14 0.15 0.05 0.21
## [7] 0.12 0.80 0.05 0.56 0.05
## [1] -156286.02 0.65 0.14 0.15 0.05 0.21
## [7] 0.12 0.80 0.05 0.56 0.05
## [1] -156326.44 0.65 0.14 0.15 0.06 0.21
## [7] 0.12 0.79 0.05 0.56 0.05
## [1] -156356.54 0.64 0.14 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] -156375.14 0.63 0.15 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] -156383.90 0.63 0.15 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160598.48 0.59 0.23 0.15 0.02 0.15
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156902.56 0.63 0.21 0.13 0.03 0.16
## [7] 0.10 0.83 0.03 0.53 0.05
## [1] -156204.76 0.65 0.19 0.13 0.03 0.17
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -156016.85 0.65 0.18 0.13 0.04 0.17
## [7] 0.12 0.81 0.03 0.55 0.04
## [1] -156002.00 0.64 0.18 0.13 0.05 0.18
## [7] 0.12 0.80 0.03 0.55 0.04
## [1] -156043.34 0.64 0.18 0.14 0.05 0.18
## [7] 0.12 0.80 0.04 0.56 0.04
## [1] -156093.86 0.63 0.18 0.14 0.05 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156135.71 0.62 0.18 0.14 0.06 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156164.05 0.61 0.18 0.15 0.06 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156179.47 0.60 0.18 0.15 0.07 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156184.52 0.59 0.19 0.15 0.07 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157324.85 0.52 0.32 0.14 0.02 0.13
## [7] 0.09 0.89 0.04 0.50 0.05
## [1] -155979.56 0.55 0.32 0.11 0.02 0.14
## [7] 0.09 0.89 0.05 0.50 0.04
## [1] -155946.33 0.56 0.32 0.09 0.03 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156007.14 0.56 0.32 0.08 0.03 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156064.73 0.57 0.32 0.08 0.04 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156103.51 0.57 0.32 0.08 0.04 0.14
## [7] 0.10 0.89 0.06 0.50 0.04
## [1] -156123.37 0.57 0.32 0.07 0.04 0.14
## [7] 0.10 0.89 0.06 0.50 0.04
## [1] -156127.64 0.56 0.32 0.07 0.05 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160447.86 0.60 0.27 0.11 0.02 0.15
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -157444.39 0.64 0.25 0.08 0.03 0.16
## [7] 0.10 0.84 0.04 0.52 0.05
## [1] -156810.33 0.65 0.24 0.07 0.04 0.17
## [7] 0.10 0.82 0.04 0.53 0.04
## [1] -156576.12 0.65 0.24 0.07 0.04 0.17
## [7] 0.11 0.80 0.05 0.53 0.04
## [1] -156520.00 0.65 0.23 0.07 0.05 0.17
## [7] 0.11 0.79 0.05 0.54 0.04
## [1] -156549.47 0.64 0.23 0.07 0.06 0.18
## [7] 0.11 0.78 0.05 0.54 0.04
## [1] -156613.32 0.63 0.24 0.07 0.06 0.18
## [7] 0.11 0.77 0.05 0.55 0.04
## [1] -156683.18 0.63 0.24 0.07 0.07 0.18
## [7] 0.12 0.76 0.05 0.55 0.04
## [1] -156744.78 0.62 0.24 0.07 0.07 0.18
## [7] 0.12 0.76 0.05 0.55 0.04
## [1] -156792.31 0.61 0.24 0.07 0.07 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156824.64 0.60 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156842.99 0.59 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156849.50 0.58 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159355.88 0.57 0.25 0.15 0.02 0.15
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -157295.65 0.62 0.23 0.12 0.03 0.16
## [7] 0.10 0.86 0.05 0.52 0.04
## [1] -156950.46 0.64 0.22 0.11 0.03 0.17
## [7] 0.11 0.85 0.06 0.52 0.04
## [1] -156835.71 0.65 0.21 0.10 0.04 0.17
## [7] 0.11 0.84 0.06 0.53 0.04
## [1] -156802.05 0.65 0.21 0.10 0.04 0.17
## [7] 0.12 0.84 0.07 0.53 0.04
## [1] -156800.34 0.65 0.20 0.10 0.05 0.17
## [7] 0.12 0.83 0.07 0.53 0.04
ggplot(sampleinfo_organoid_fetal, aes(as.numeric(as.character(passage.or.rescope.no_numeric)), thresholded_prior_I))+
geom_point(size=2,shape=21,color="black",aes(fill=as.factor(passage.or.rescope.no_numeric)))+xlab("Passage")+
ylab("Intermediate Peak Prior")+theme_bw()+theme(axis.title = element_text(size=12))+
#geom_text(aes(label=count, vjust=vjust, hjust=hjust), color="grey40", size=3)+
scale_x_continuous(breaks=c(1,2,3,4,6,7,8,2,4,10,11,14,16))+ scale_fill_manual(values=pass_col,name="Passage\nNumber", guide=F)
ggsave(here("figs","MTAB4957_fetal_mixture_model_prior_I.pdf"), width=3, height=2)
sampleinfo_organoid_fetal$thresholded_prior10<-F
sampleinfo_organoid_fetal$thresholded_prior10[which(sampleinfo_organoid_fetal$thresholded_prior_I>0.10)]<-T
percent_passing<-round((tapply(sampleinfo_organoid_fetal$thresholded_prior10, sampleinfo_organoid_fetal$passage.or.rescope.no_numeric, sum)/tapply(sampleinfo_organoid_fetal$array.id, sampleinfo_organoid_fetal$passage.or.rescope.no_numeric, length))*100,2)
passed_num<-tapply(sampleinfo_organoid_fetal$thresholded_prior10, sampleinfo_organoid_fetal$passage.or.rescope.no_numeric, sum)
org_numer<-tapply(sampleinfo_organoid_fetal$array.id, sampleinfo_organoid_fetal$passage.or.rescope.no_numeric, length)
df<-data.frame(passage=names(percent_passing), passing=percent_passing, pro_passing=percent_passing/100, count=org_numer, passed_num=passed_num)
df$passage.factor <- factor(df$passage, levels = c(23,21,14,12,9,7,6,5,3,2,1))
df<-cbind(df,(binom.confint(df$passed_num, df$count, method="exact", conf.level=0.95)))
df$upper<-df$upper*100
df$lower<-df$lower*100
ggplot(df, aes(as.numeric(as.character(passage)), passing))+
geom_errorbar(aes(ymin=lower, ymax=upper), colour="grey70", width=.25)+
geom_line(color="grey20")+geom_point(size=1.25,shape=21,color="black",aes(fill=passage.factor))+xlab("Passage")+
ylab("Samples with Trimodal\nDistribution (%)")+theme_bw()+theme(axis.title = element_text(size=10))+
scale_x_continuous(breaks=c(1,2,3,4,6,7,8,2,4,10,11,14,16))+ scale_fill_manual(values=pass_col,name="Passage\nNumber", guide=F)
ggsave(here("figs","MTAB4957_fetal_mixture_model_prior_I_threshold.pdf"), width=3, height=2)
## plot all samples
plts_paired<-lapply(1:nrow(sampleinfo_organoid_fetal), function(x){
passage<-paste("passage: ",sampleinfo_organoid_fetal$passage.or.rescope.no_numeric[x],"\nIndividual: ", sampleinfo_organoid_fetal$Characteristics.individual.[x],"\nPrior I: " ,round(sampleinfo_organoid_fetal$thresholded_prior_I[x],2), sep="")
converted<-as.numeric(round(MTAB4957_beta_VeryVariable[,x]*1000,0))
counts<-rep(1000, length(converted))
res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
draw_fit_params_gg(converted, counts, res,passage)
})
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157952.80 0.56 0.28 0.14 0.02 0.14
## [7] 0.10 0.89 0.04 0.50 0.04
## [1] -156833.59 0.60 0.27 0.11 0.03 0.15
## [7] 0.11 0.88 0.05 0.50 0.04
## [1] -156790.71 0.61 0.26 0.09 0.04 0.16
## [7] 0.12 0.88 0.06 0.50 0.04
## [1] -156840.30 0.62 0.26 0.08 0.04 0.16
## [7] 0.13 0.87 0.06 0.50 0.04
## [1] -156896.56 0.62 0.25 0.07 0.05 0.17
## [7] 0.13 0.87 0.06 0.51 0.04
## [1] -156941.22 0.62 0.25 0.07 0.05 0.17
## [7] 0.14 0.87 0.07 0.51 0.03
## [1] -156971.46 0.62 0.25 0.07 0.06 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] -156989.01 0.62 0.25 0.07 0.06 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] -156996.69 0.62 0.25 0.06 0.07 0.17
## [7] 0.14 0.87 0.07 0.51 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159957.90 0.58 0.16 0.24 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -156245.96 0.62 0.12 0.24 0.03 0.19
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155479.65 0.63 0.10 0.24 0.03 0.21
## [7] 0.12 0.84 0.03 0.55 0.05
## [1] -155229.53 0.62 0.09 0.25 0.04 0.23
## [7] 0.13 0.83 0.04 0.56 0.05
## [1] -155159.03 0.62 0.08 0.26 0.04 0.24
## [7] 0.13 0.83 0.04 0.56 0.04
## [1] -155158.76 0.61 0.08 0.26 0.05 0.25
## [7] 0.14 0.83 0.04 0.57 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -156851.65 0.52 0.33 0.14 0.02 0.13
## [7] 0.10 0.90 0.04 0.49 0.04
## [1] -155883.29 0.54 0.33 0.11 0.02 0.14
## [7] 0.10 0.90 0.05 0.49 0.04
## [1] -155955.77 0.55 0.33 0.09 0.03 0.14
## [7] 0.11 0.90 0.06 0.49 0.04
## [1] -156103.00 0.55 0.33 0.09 0.03 0.14
## [7] 0.11 0.90 0.06 0.49 0.04
## [1] -156234.08 0.55 0.33 0.08 0.04 0.15
## [7] 0.11 0.90 0.06 0.48 0.04
## [1] -156336.91 0.55 0.33 0.08 0.04 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156414.40 0.55 0.33 0.08 0.04 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156471.91 0.55 0.33 0.08 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156514.21 0.55 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156544.96 0.54 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.05 0.48 0.04
## [1] -156566.80 0.54 0.33 0.07 0.05 0.15
## [7] 0.12 0.91 0.04 0.48 0.04
## [1] -156581.56 0.54 0.33 0.07 0.06 0.15
## [7] 0.12 0.91 0.04 0.48 0.04
## [1] -156590.50 0.53 0.33 0.07 0.06 0.15
## [7] 0.12 0.92 0.04 0.48 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -155944.91 0.46 0.43 0.10 0.01 0.11
## [7] 0.08 0.89 0.04 0.48 0.05
## [1] -154340.82 0.44 0.47 0.07 0.01 0.12
## [7] 0.07 0.90 0.05 0.47 0.05
## [1] -154158.94 0.44 0.49 0.06 0.02 0.12
## [7] 0.08 0.90 0.05 0.46 0.04
## [1] -154209.89 0.43 0.50 0.05 0.02 0.12
## [7] 0.08 0.90 0.05 0.46 0.04
## [1] -154316.43 0.43 0.50 0.05 0.02 0.12
## [7] 0.08 0.90 0.04 0.46 0.04
## [1] -154428.61 0.42 0.51 0.05 0.02 0.13
## [7] 0.08 0.90 0.04 0.45 0.04
## [1] -154529.96 0.42 0.51 0.05 0.02 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154615.48 0.42 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154684.35 0.41 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154737.29 0.41 0.51 0.05 0.03 0.13
## [7] 0.08 0.91 0.04 0.45 0.04
## [1] -154775.57 0.41 0.52 0.05 0.03 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154800.67 0.40 0.52 0.05 0.03 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154814.12 0.40 0.52 0.05 0.04 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] -154817.44 0.40 0.52 0.05 0.04 0.13
## [7] 0.08 0.91 0.03 0.45 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -156833.58 0.51 0.39 0.09 0.02 0.12
## [7] 0.09 0.88 0.04 0.49 0.04
## [1] -155662.25 0.51 0.41 0.05 0.02 0.13
## [7] 0.09 0.88 0.05 0.48 0.04
## [1] -155583.43 0.51 0.42 0.04 0.03 0.13
## [7] 0.10 0.87 0.05 0.47 0.04
## [1] -155650.18 0.51 0.43 0.03 0.03 0.14
## [7] 0.10 0.87 0.06 0.47 0.04
## [1] -155738.30 0.50 0.44 0.03 0.04 0.14
## [7] 0.11 0.87 0.06 0.47 0.03
## [1] -155815.07 0.49 0.44 0.02 0.04 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155871.96 0.49 0.45 0.02 0.05 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155908.99 0.48 0.45 0.02 0.05 0.14
## [7] 0.11 0.87 0.06 0.46 0.03
## [1] -155929.26 0.47 0.45 0.02 0.06 0.14
## [7] 0.12 0.87 0.06 0.46 0.03
## [1] -155936.55 0.47 0.45 0.02 0.06 0.14
## [7] 0.12 0.87 0.06 0.46 0.03
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157509.21 0.54 0.25 0.19 0.02 0.13
## [7] 0.11 0.88 0.04 0.51 0.05
## [1] -156447.22 0.59 0.22 0.17 0.03 0.14
## [7] 0.12 0.87 0.04 0.52 0.04
## [1] -156309.10 0.61 0.21 0.16 0.03 0.14
## [7] 0.12 0.87 0.05 0.53 0.04
## [1] -156309.49 0.62 0.20 0.15 0.04 0.14
## [7] 0.13 0.86 0.05 0.53 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158735.16 0.57 0.29 0.11 0.02 0.13
## [7] 0.11 0.87 0.04 0.50 0.05
## [1] -157318.31 0.62 0.28 0.08 0.03 0.15
## [7] 0.12 0.86 0.05 0.51 0.04
## [1] -157020.94 0.63 0.27 0.06 0.04 0.15
## [7] 0.13 0.84 0.06 0.51 0.04
## [1] -156896.01 0.64 0.27 0.05 0.04 0.16
## [7] 0.14 0.83 0.07 0.51 0.04
## [1] -156839.73 0.64 0.26 0.05 0.05 0.16
## [7] 0.14 0.81 0.07 0.51 0.04
## [1] -156818.76 0.63 0.26 0.04 0.06 0.17
## [7] 0.15 0.80 0.07 0.51 0.04
## [1] -156816.96 0.63 0.26 0.04 0.06 0.17
## [7] 0.15 0.79 0.07 0.52 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160911.83 0.60 0.22 0.16 0.02 0.15
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -157068.71 0.64 0.19 0.14 0.03 0.17
## [7] 0.11 0.83 0.03 0.53 0.05
## [1] -156304.49 0.66 0.17 0.14 0.03 0.18
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -156080.52 0.66 0.16 0.14 0.04 0.19
## [7] 0.12 0.81 0.03 0.54 0.05
## [1] -156045.71 0.65 0.16 0.14 0.05 0.19
## [7] 0.13 0.80 0.03 0.55 0.05
## [1] -156076.03 0.65 0.16 0.14 0.05 0.20
## [7] 0.13 0.80 0.04 0.55 0.05
## [1] -156120.64 0.64 0.16 0.15 0.05 0.20
## [7] 0.13 0.79 0.04 0.56 0.05
## [1] -156159.66 0.63 0.16 0.15 0.06 0.20
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156187.17 0.62 0.16 0.15 0.06 0.21
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156203.21 0.61 0.16 0.16 0.06 0.21
## [7] 0.14 0.79 0.04 0.56 0.05
## [1] -156209.91 0.60 0.17 0.16 0.07 0.21
## [7] 0.14 0.78 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -161638.23 0.62 0.19 0.16 0.02 0.17
## [7] 0.09 0.85 0.03 0.51 0.05
## [1] -157151.06 0.67 0.16 0.14 0.03 0.20
## [7] 0.10 0.83 0.03 0.53 0.05
## [1] -156228.56 0.68 0.14 0.14 0.04 0.21
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -155932.47 0.68 0.14 0.14 0.05 0.23
## [7] 0.11 0.81 0.03 0.54 0.05
## [1] -155865.39 0.67 0.13 0.14 0.05 0.24
## [7] 0.12 0.80 0.03 0.55 0.04
## [1] -155884.50 0.66 0.13 0.15 0.06 0.25
## [7] 0.12 0.79 0.04 0.55 0.04
## [1] -155928.35 0.65 0.13 0.15 0.07 0.25
## [7] 0.12 0.79 0.04 0.56 0.04
## [1] -155970.79 0.64 0.13 0.16 0.07 0.26
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156002.60 0.63 0.14 0.16 0.07 0.26
## [7] 0.13 0.78 0.04 0.56 0.04
## [1] -156022.41 0.62 0.14 0.16 0.08 0.26
## [7] 0.13 0.78 0.04 0.56 0.05
## [1] -156032.00 0.61 0.14 0.17 0.08 0.26
## [7] 0.13 0.78 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159328.07 0.58 0.22 0.18 0.02 0.15
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -157270.96 0.63 0.19 0.16 0.03 0.16
## [7] 0.11 0.86 0.05 0.53 0.05
## [1] -156822.75 0.65 0.17 0.15 0.03 0.17
## [7] 0.12 0.85 0.05 0.53 0.05
## [1] -156667.50 0.66 0.16 0.15 0.04 0.18
## [7] 0.13 0.84 0.06 0.54 0.05
## [1] -156628.51 0.66 0.15 0.15 0.04 0.18
## [7] 0.14 0.83 0.06 0.55 0.05
## [1] -156636.20 0.66 0.15 0.15 0.05 0.19
## [7] 0.14 0.83 0.06 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159121.75 0.57 0.27 0.13 0.02 0.14
## [7] 0.10 0.88 0.04 0.51 0.05
## [1] -157287.07 0.62 0.25 0.10 0.03 0.15
## [7] 0.10 0.86 0.05 0.52 0.04
## [1] -156927.53 0.64 0.24 0.09 0.03 0.15
## [7] 0.11 0.84 0.06 0.52 0.04
## [1] -156795.47 0.65 0.23 0.08 0.04 0.16
## [7] 0.12 0.83 0.06 0.53 0.04
## [1] -156752.57 0.65 0.23 0.08 0.05 0.16
## [7] 0.12 0.82 0.07 0.53 0.04
## [1] -156748.57 0.65 0.23 0.07 0.05 0.16
## [7] 0.12 0.81 0.07 0.54 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158970.73 0.57 0.17 0.24 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155944.77 0.60 0.14 0.24 0.02 0.18
## [7] 0.10 0.86 0.03 0.53 0.05
## [1] -155446.62 0.61 0.12 0.24 0.03 0.20
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155283.74 0.61 0.11 0.24 0.03 0.21
## [7] 0.12 0.85 0.04 0.55 0.04
## [1] -155234.20 0.61 0.11 0.24 0.04 0.21
## [7] 0.13 0.84 0.04 0.56 0.04
## [1] -155231.43 0.61 0.10 0.25 0.04 0.22
## [7] 0.13 0.84 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160493.51 0.60 0.20 0.18 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156915.39 0.64 0.16 0.17 0.03 0.18
## [7] 0.11 0.84 0.03 0.53 0.05
## [1] -156233.18 0.66 0.14 0.16 0.04 0.20
## [7] 0.12 0.83 0.03 0.54 0.04
## [1] -156012.04 0.66 0.14 0.16 0.04 0.21
## [7] 0.12 0.82 0.04 0.54 0.04
## [1] -155955.34 0.66 0.13 0.17 0.05 0.22
## [7] 0.13 0.82 0.04 0.55 0.04
## [1] -155961.94 0.65 0.13 0.17 0.05 0.22
## [7] 0.13 0.81 0.04 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157985.66 0.55 0.15 0.29 0.02 0.17
## [7] 0.10 0.88 0.03 0.52 0.05
## [1] -155299.24 0.57 0.11 0.29 0.02 0.19
## [7] 0.11 0.87 0.03 0.53 0.05
## [1] -154836.67 0.58 0.10 0.30 0.03 0.21
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -154674.82 0.58 0.09 0.30 0.03 0.23
## [7] 0.12 0.86 0.04 0.55 0.05
## [1] -154618.80 0.58 0.08 0.31 0.04 0.24
## [7] 0.13 0.85 0.04 0.55 0.05
## [1] -154608.82 0.57 0.08 0.31 0.04 0.25
## [7] 0.14 0.85 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160561.43 0.60 0.20 0.18 0.02 0.16
## [7] 0.10 0.86 0.03 0.51 0.05
## [1] -156977.58 0.64 0.17 0.17 0.03 0.19
## [7] 0.10 0.85 0.03 0.52 0.05
## [1] -156307.57 0.65 0.15 0.16 0.03 0.20
## [7] 0.11 0.83 0.04 0.53 0.05
## [1] -156095.62 0.66 0.14 0.16 0.04 0.21
## [7] 0.12 0.82 0.04 0.54 0.05
## [1] -156041.74 0.65 0.14 0.16 0.04 0.22
## [7] 0.12 0.82 0.04 0.55 0.05
## [1] -156046.58 0.65 0.13 0.17 0.05 0.22
## [7] 0.13 0.81 0.04 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158513.30 0.55 0.18 0.25 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155730.90 0.59 0.15 0.24 0.02 0.17
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155309.77 0.60 0.13 0.24 0.03 0.19
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -155174.71 0.60 0.12 0.25 0.03 0.19
## [7] 0.12 0.85 0.03 0.55 0.05
## [1] -155134.73 0.60 0.12 0.25 0.04 0.20
## [7] 0.13 0.85 0.04 0.55 0.05
## [1] -155134.08 0.60 0.11 0.25 0.04 0.21
## [7] 0.13 0.85 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158305.37 0.55 0.16 0.27 0.02 0.16
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155475.57 0.58 0.12 0.27 0.02 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155024.67 0.59 0.11 0.27 0.03 0.20
## [7] 0.12 0.86 0.03 0.54 0.05
## [1] -154871.25 0.59 0.10 0.27 0.03 0.22
## [7] 0.13 0.85 0.03 0.54 0.05
## [1] -154818.39 0.59 0.09 0.28 0.04 0.23
## [7] 0.14 0.85 0.04 0.55 0.05
## [1] -154808.34 0.59 0.09 0.28 0.04 0.24
## [7] 0.15 0.85 0.04 0.55 0.05
## [1] -154816.04 0.58 0.09 0.28 0.05 0.24
## [7] 0.15 0.85 0.04 0.55 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159623.23 0.58 0.17 0.23 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -156433.23 0.62 0.13 0.22 0.03 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155803.37 0.63 0.12 0.22 0.03 0.21
## [7] 0.12 0.85 0.04 0.54 0.05
## [1] -155575.47 0.64 0.11 0.22 0.04 0.22
## [7] 0.12 0.84 0.04 0.55 0.05
## [1] -155500.97 0.63 0.10 0.22 0.04 0.24
## [7] 0.13 0.84 0.04 0.56 0.05
## [1] -155492.92 0.63 0.10 0.23 0.05 0.25
## [7] 0.13 0.83 0.05 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -158766.69 0.56 0.16 0.26 0.02 0.17
## [7] 0.10 0.87 0.03 0.52 0.05
## [1] -155655.89 0.59 0.12 0.26 0.02 0.19
## [7] 0.11 0.86 0.03 0.53 0.05
## [1] -155129.24 0.60 0.10 0.26 0.03 0.21
## [7] 0.12 0.85 0.03 0.54 0.05
## [1] -154945.49 0.60 0.10 0.27 0.04 0.23
## [7] 0.13 0.85 0.03 0.55 0.05
## [1] -154883.58 0.60 0.09 0.27 0.04 0.24
## [7] 0.14 0.85 0.04 0.55 0.05
## [1] -154874.84 0.59 0.09 0.27 0.04 0.25
## [7] 0.14 0.84 0.04 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160347.69 0.59 0.18 0.21 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156640.87 0.63 0.14 0.20 0.03 0.18
## [7] 0.11 0.84 0.03 0.53 0.05
## [1] -155891.20 0.64 0.13 0.21 0.03 0.20
## [7] 0.12 0.83 0.03 0.54 0.05
## [1] -155664.02 0.64 0.12 0.21 0.04 0.21
## [7] 0.13 0.83 0.03 0.55 0.05
## [1] -155610.24 0.64 0.11 0.21 0.04 0.22
## [7] 0.14 0.82 0.04 0.55 0.05
## [1] -155616.55 0.63 0.11 0.22 0.04 0.22
## [7] 0.14 0.82 0.04 0.56 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160298.78 0.59 0.18 0.22 0.02 0.16
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156360.09 0.62 0.14 0.21 0.03 0.18
## [7] 0.11 0.85 0.03 0.54 0.05
## [1] -155596.90 0.63 0.12 0.22 0.03 0.19
## [7] 0.11 0.83 0.03 0.55 0.05
## [1] -155368.14 0.63 0.11 0.22 0.04 0.20
## [7] 0.12 0.83 0.04 0.56 0.05
## [1] -155322.88 0.63 0.10 0.23 0.04 0.21
## [7] 0.13 0.82 0.04 0.57 0.04
## [1] -155342.87 0.62 0.10 0.23 0.05 0.21
## [7] 0.13 0.82 0.04 0.57 0.04
## [1] -155380.85 0.61 0.10 0.24 0.05 0.22
## [7] 0.13 0.82 0.04 0.58 0.04
## [1] -155418.05 0.60 0.10 0.24 0.05 0.22
## [7] 0.14 0.81 0.04 0.58 0.04
## [1] -155448.12 0.60 0.10 0.25 0.06 0.22
## [7] 0.14 0.81 0.04 0.58 0.04
## [1] -155470.00 0.59 0.10 0.25 0.06 0.22
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] -155484.68 0.58 0.10 0.25 0.06 0.23
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] -155493.69 0.57 0.11 0.26 0.06 0.23
## [7] 0.14 0.81 0.05 0.58 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160906.11 0.60 0.21 0.17 0.02 0.16
## [7] 0.09 0.86 0.04 0.52 0.05
## [1] -157285.13 0.65 0.18 0.15 0.03 0.18
## [7] 0.10 0.84 0.04 0.53 0.05
## [1] -156526.19 0.66 0.16 0.14 0.03 0.19
## [7] 0.10 0.83 0.04 0.54 0.05
## [1] -156276.29 0.67 0.15 0.14 0.04 0.20
## [7] 0.11 0.82 0.04 0.55 0.05
## [1] -156222.17 0.66 0.15 0.14 0.05 0.21
## [7] 0.11 0.81 0.04 0.55 0.05
## [1] -156243.48 0.66 0.14 0.15 0.05 0.21
## [7] 0.12 0.80 0.05 0.56 0.05
## [1] -156286.02 0.65 0.14 0.15 0.05 0.21
## [7] 0.12 0.80 0.05 0.56 0.05
## [1] -156326.44 0.65 0.14 0.15 0.06 0.21
## [7] 0.12 0.79 0.05 0.56 0.05
## [1] -156356.54 0.64 0.14 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] -156375.14 0.63 0.15 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] -156383.90 0.63 0.15 0.16 0.06 0.22
## [7] 0.12 0.79 0.05 0.57 0.05
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160598.48 0.59 0.23 0.15 0.02 0.15
## [7] 0.10 0.86 0.03 0.52 0.05
## [1] -156902.56 0.63 0.21 0.13 0.03 0.16
## [7] 0.10 0.83 0.03 0.53 0.05
## [1] -156204.76 0.65 0.19 0.13 0.03 0.17
## [7] 0.11 0.82 0.03 0.54 0.05
## [1] -156016.85 0.65 0.18 0.13 0.04 0.17
## [7] 0.12 0.81 0.03 0.55 0.04
## [1] -156002.00 0.64 0.18 0.13 0.05 0.18
## [7] 0.12 0.80 0.03 0.55 0.04
## [1] -156043.34 0.64 0.18 0.14 0.05 0.18
## [7] 0.12 0.80 0.04 0.56 0.04
## [1] -156093.86 0.63 0.18 0.14 0.05 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156135.71 0.62 0.18 0.14 0.06 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156164.05 0.61 0.18 0.15 0.06 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156179.47 0.60 0.18 0.15 0.07 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] -156184.52 0.59 0.19 0.15 0.07 0.18
## [7] 0.13 0.79 0.04 0.56 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -157324.85 0.52 0.32 0.14 0.02 0.13
## [7] 0.09 0.89 0.04 0.50 0.05
## [1] -155979.56 0.55 0.32 0.11 0.02 0.14
## [7] 0.09 0.89 0.05 0.50 0.04
## [1] -155946.33 0.56 0.32 0.09 0.03 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156007.14 0.56 0.32 0.08 0.03 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156064.73 0.57 0.32 0.08 0.04 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] -156103.51 0.57 0.32 0.08 0.04 0.14
## [7] 0.10 0.89 0.06 0.50 0.04
## [1] -156123.37 0.57 0.32 0.07 0.04 0.14
## [7] 0.10 0.89 0.06 0.50 0.04
## [1] -156127.64 0.56 0.32 0.07 0.05 0.14
## [7] 0.09 0.89 0.06 0.50 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -160447.86 0.60 0.27 0.11 0.02 0.15
## [7] 0.09 0.86 0.04 0.51 0.05
## [1] -157444.39 0.64 0.25 0.08 0.03 0.16
## [7] 0.10 0.84 0.04 0.52 0.05
## [1] -156810.33 0.65 0.24 0.07 0.04 0.17
## [7] 0.10 0.82 0.04 0.53 0.04
## [1] -156576.12 0.65 0.24 0.07 0.04 0.17
## [7] 0.11 0.80 0.05 0.53 0.04
## [1] -156520.00 0.65 0.23 0.07 0.05 0.17
## [7] 0.11 0.79 0.05 0.54 0.04
## [1] -156549.47 0.64 0.23 0.07 0.06 0.18
## [7] 0.11 0.78 0.05 0.54 0.04
## [1] -156613.32 0.63 0.24 0.07 0.06 0.18
## [7] 0.11 0.77 0.05 0.55 0.04
## [1] -156683.18 0.63 0.24 0.07 0.07 0.18
## [7] 0.12 0.76 0.05 0.55 0.04
## [1] -156744.78 0.62 0.24 0.07 0.07 0.18
## [7] 0.12 0.76 0.05 0.55 0.04
## [1] -156792.31 0.61 0.24 0.07 0.07 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156824.64 0.60 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156842.99 0.59 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] -156849.50 0.58 0.25 0.08 0.08 0.18
## [7] 0.12 0.75 0.05 0.55 0.04
## [1] "loglik" "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"
## [7] "Rho(U)" "MU(M)" "Rho(M)" "mu_I" "rho_I"
## [1] "XXX" "0.41" "0.31" "0.27" "0.01" "0.1" "0.1" "0.9" "0.03" "0.5"
## [11] "0.05"
## [1] -159355.88 0.57 0.25 0.15 0.02 0.15
## [7] 0.09 0.88 0.04 0.51 0.05
## [1] -157295.65 0.62 0.23 0.12 0.03 0.16
## [7] 0.10 0.86 0.05 0.52 0.04
## [1] -156950.46 0.64 0.22 0.11 0.03 0.17
## [7] 0.11 0.85 0.06 0.52 0.04
## [1] -156835.71 0.65 0.21 0.10 0.04 0.17
## [7] 0.11 0.84 0.06 0.53 0.04
## [1] -156802.05 0.65 0.21 0.10 0.04 0.17
## [7] 0.12 0.84 0.07 0.53 0.04
## [1] -156800.34 0.65 0.20 0.10 0.05 0.17
## [7] 0.12 0.83 0.07 0.53 0.04
plts_paired_order<-plts_paired[order(sampleinfo_organoid_fetal$passage.or.rescope.no_numeric)]
pdf(here("figs","MTAB4957_fetal_organoids_thresholding_all_samples.pdf"))
plts_paired_order
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
##
## [[5]]
##
## [[6]]
##
## [[7]]
##
## [[8]]
##
## [[9]]
##
## [[10]]
##
## [[11]]
##
## [[12]]
##
## [[13]]
##
## [[14]]
##
## [[15]]
##
## [[16]]
##
## [[17]]
##
## [[18]]
##
## [[19]]
##
## [[20]]
##
## [[21]]
##
## [[22]]
##
## [[23]]
##
## [[24]]
##
## [[25]]
##
## [[26]]
dev.off()
## png
## 2
mod<-model.matrix(~ 0 + passage.or.rescope.no_numeric, data=sampleinfo_organoid_notfetal)
fit <- lmFit(MTAB_organoid_beta_notfetal, mod)
ebfit <- eBayes(fit)
# covariate adjusted beta values
beta<-MTAB_organoid_beta_notfetal
passage_db<-sapply(1:nrow(beta), function(x){
sampleinfo_cpg<-sampleinfo_organoid_notfetal
sampleinfo_cpg$beta<-as.numeric(beta[x,])
fit<-lm(beta ~ passage.or.rescope.no_numeric, data=sampleinfo_cpg)
pval<-summary(fit)$coef["passage.or.rescope.no_numeric","Pr(>|t|)"]
slope<-fit$coefficients[2]
(min(sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric)*slope) - (max(sampleinfo_organoid_notfetal$passage.or.rescope.no_numeric)*slope)})
passage_MTAB<-data.frame(p.value=ebfit$p.value[,"passage.or.rescope.no_numeric"], CpG=rownames(beta), db=passage_db)
# Adjust P values
passage_MTAB$p_adjusted<-p.adjust(passage_MTAB$p.value, method="BH")
diff_CpG_dbMTAB<-passage_MTAB[which(passage_MTAB$p_adjusted<0.05 & abs(passage_MTAB$db)>0.15),] #25086
diff_CpG_db_hypoMTAB<-diff_CpG_dbMTAB$CpG[which((diff_CpG_dbMTAB$db)>=0.15)] # 17419
diff_CpG_db_hyperMTAB<-diff_CpG_dbMTAB$CpG[which((diff_CpG_dbMTAB$db)<=(-0.15))] # 7667
load(here("data","beta_organoids.RData"))
pvals_long<-read.csv(here("data","Heteroskedactiy_pvalues_FDR_1000iter.csv"), header=T)
pvals_long[,1]<-NULL
colnames(pvals_long)<-c("BP_count","diff_count","mean_db","fdr_BP","fdr_diff")
pvals_long$CpG<-rownames(organoid_beta)
pvals_long$BP_pval<-((1000-pvals_long$BP_count)+1)/1001
pvals_long$diff_pval<-((1000-pvals_long$diff_count)+1)/1001
pvals_long$BP_fdr<-((1000-pvals_long$fdr_BP)+1)/1001
pvals_long$diff_fdr<-((1000-pvals_long$fdr_diff)+1)/1001
hetero_CpG<-rownames(organoid_beta)[which(pvals_long$BP_fdr<0.05)]
print(paste("CpGs with significant (adjusted p<0.05) heteroskedactiy: ", length(hetero_CpG), sep=""))
## [1] "CpGs with significant (adjusted p<0.05) heteroskedactiy: 41852"
diff_CpG<-rownames(organoid_beta)[which(pvals_long$diff_fdr<0.05)]
diff_CpG_db<-pvals_long[which(pvals_long$diff_fdr<0.05 & abs(pvals_long$mean_db)>0.15),]
print(paste("CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: ", nrow(diff_CpG_db), sep=""))
## [1] "CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: 23766"
diff_CpG_db_hypo<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)>=0.15)] # 11772
diff_CpG_db_hyper<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)<=(-0.15))] # 5214
How many differential CpGs could overlap? 450K vs EPIC
print(paste("Of the ", nrow(diff_CpG_db), " CpGs differential with passage in the original organoids, ",
length(diff_CpG_db$CpG[which(diff_CpG_db$CpG%in%rownames(MTAB_organoid_beta_notfetal))]), " are in the 450K data", sep=""))
## [1] "Of the 23766 CpGs differential with passage in the original organoids, 7628 are in the 450K data"
diff_CpG_db_hypo_overlap<-diff_CpG_db_hypo[which(diff_CpG_db_hypo%in%rownames(MTAB_organoid_beta_notfetal))]
diff_CpG_db_hyper_overlap<-diff_CpG_db_hyper[which(diff_CpG_db_hyper%in%rownames(MTAB_organoid_beta_notfetal))]
diff_CpG_db_hypoMTAB_overlap<-diff_CpG_db_hypoMTAB[which(diff_CpG_db_hypoMTAB%in%pvals_long$CpG)]
diff_CpG_db_hyperMTAB_overlap<-diff_CpG_db_hyperMTAB[which(diff_CpG_db_hyperMTAB%in%pvals_long$CpG)]
print(paste("Of the ",length(diff_CpG_db_hypo_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap))," are also hypo in the MTAB-4957 cohort (",
round((length(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap))/length(diff_CpG_db_hypo_overlap))*100,2),"%)",sep=""))
## [1] "Of the 5098 hypo CpGs also on the 450K 3550 are also hypo in the MTAB-4957 cohort (69.64%)"
print(paste("Of the ",length(diff_CpG_db_hyper_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap))," are also hypo in the MTAB-4957 cohort (",
round((length(intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap))/length(diff_CpG_db_hyper_overlap))*100,2),"%)",sep=""))
## [1] "Of the 2530 hypo CpGs also on the 450K 1198 are also hypo in the MTAB-4957 cohort (47.35%)"
plt_db_direction<-merge(pvals_long[,c(3,6)], passage_MTAB, by="CpG")# 380776
plt_db_direction$sig<-"Not Significant"
plt_db_direction$sig[which(plt_db_direction$CpG%in%c(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap),intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap)))]<-"Significant\nIn Both\nCohorts"
ggplot(plt_db_direction, aes(mean_db, db))+geom_point(aes(color=sig, alpha=sig),shape=19)+th+theme_bw()+
scale_color_manual(values=c("lightgrey", "cornflowerblue"), name="Significant\nWith Passage")+
scale_alpha_manual(values=c(0.25,1), guide=F)+
geom_hline(yintercept=c(-0.15,0.15), color="grey60")+geom_vline(xintercept=c(-0.15,0.15), color="grey60")+
ylim(-0.8,0.8)+xlim(-0.8,0.8)+xlab("Original Organoid\nPassage Delta Beta")+ylab("MTAB-4957 Organoid\nPassage Delta Beta")+
stat_smooth(method="lm", se=F, color="black")
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
ggsave(here("figs","MTAB_db_directionality.pdf"), width=5, height=3.75)
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
ggsave(here("figs/jpeg","MTAB_db_directionality.jpeg"), width=5, height=3.75)
## Warning: Removed 1 rows containing non-finite values (stat_smooth).
## Warning: Removed 1 rows containing missing values (geom_point).
print(paste("Correlation of delta betas between cohorts: ", round(cor(plt_db_direction$db, plt_db_direction$mean_db),2), sep=""))
## [1] "Correlation of delta betas between cohorts: 0.53"
epic.organoid_minimal<-epic.organoid[,c(2, 14, 17)]
colnames(epic.organoid_minimal)[1]<-"Assay.Name"
epic.organoid_minimal$cohort<-"Original Organoids"
sampleinfo_organoid_notfetal_minimal<-sampleinfo_organoid_notfetal[,c(16,22,21)]
sampleinfo_organoid_notfetal_minimal$cohort<-"MTAB-4957 Organoids"
sample_info_both<-rbind(sampleinfo_organoid_notfetal_minimal,epic.organoid_minimal)
plt_hetero_MTAB<-function(CpGs, legend, axislab, title){
betas<-melt(cbind(MTAB_organoid_beta_notfetal[CpGs,],organoid_beta[CpGs,]))
organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")
p<-ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
geom_line(aes(group=sample_ID),color="lightgrey")+
stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
facet_grid(cohort~Var1)+
ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
xlim(1,16)
if(missing(legend) & missing(axislab) & missing(title)){p}else{
if(legend=="N" & axislab=="N"){p + theme(legend.position = "none",axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())+ ggtitle(title)}else{
if(legend=="N" & axislab=="Y"){p + theme(legend.position = "none") + ggtitle(title)}}}}
plt_hetero_MTAB(c("cg25402228","cg09146328"))
ggsave(here("figs","Passage_differential_CpGs_MTAB4957.pdf"),width = 4.75, height = 4)
ggsave(here("figs/jpeg","Passage_differential_CpGs_MTAB4957.jpeg"), width = 4.75, height = 4)
mod<-model.matrix(~ 0 + passage.or.rescope.no_numeric, data=sampleinfo_organoid_fetal)
fit <- lmFit(MTAB_organoid_beta_fetal, mod)
ebfit <- eBayes(fit)
# covariate adjusted beta values
beta<-MTAB_organoid_beta_fetal
passage_db<-sapply(1:nrow(beta), function(x){
sampleinfo_cpg<-sampleinfo_organoid_fetal
sampleinfo_cpg$beta<-as.numeric(beta[x,])
fit<-lm(beta ~ passage.or.rescope.no_numeric, data=sampleinfo_cpg)
pval<-summary(fit)$coef["passage.or.rescope.no_numeric","Pr(>|t|)"]
slope<-fit$coefficients[2]
(min(sampleinfo_organoid_fetal$passage.or.rescope.no_numeric)*slope) - (max(sampleinfo_organoid_fetal$passage.or.rescope.no_numeric)*slope)})
passage_MTAB<-data.frame(p.value=ebfit$p.value[,"passage.or.rescope.no_numeric"], CpG=rownames(beta), db=passage_db)
# p adjust
passage_MTAB$p_adjusted<-p.adjust(passage_MTAB$p.value, method="BH")
diff_CpG_dbMTAB<-passage_MTAB[which(passage_MTAB$p_adjusted<0.05 & abs(passage_MTAB$db)>0.15),] #58958
diff_CpG_db_hypoMTAB<-diff_CpG_dbMTAB$CpG[which((diff_CpG_dbMTAB$db)>=0.15)] # 45098
diff_CpG_db_hyperMTAB<-diff_CpG_dbMTAB$CpG[which((diff_CpG_dbMTAB$db)<=(-0.15))] # 13860
How many differential CpGs could overlap? 450K vs EPIC
print(paste("Of the ", nrow(diff_CpG_db), " CpGs differential with passage in the original organoids, ",
length(diff_CpG_db$CpG[which(diff_CpG_db$CpG%in%rownames(MTAB_organoid_beta_fetal))]), " are in the 450K data", sep=""))
## [1] "Of the 23766 CpGs differential with passage in the original organoids, 7628 are in the 450K data"
diff_CpG_db_hypo_overlap<-diff_CpG_db_hypo[which(diff_CpG_db_hypo%in%rownames(MTAB_organoid_beta_fetal))]
diff_CpG_db_hyper_overlap<-diff_CpG_db_hyper[which(diff_CpG_db_hyper%in%rownames(MTAB_organoid_beta_fetal))]
diff_CpG_db_hypoMTAB_overlap<-diff_CpG_db_hypoMTAB[which(diff_CpG_db_hypoMTAB%in%pvals_long$CpG)]
diff_CpG_db_hyperMTAB_overlap<-diff_CpG_db_hyperMTAB[which(diff_CpG_db_hyperMTAB%in%pvals_long$CpG)]
print(paste("Of the ",length(diff_CpG_db_hypo_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap))," are also hypo in the MTAB-4957 cohort (",
round((length(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap))/length(diff_CpG_db_hypo_overlap))*100,2),"%)",sep=""))
## [1] "Of the 5098 hypo CpGs also on the 450K 3980 are also hypo in the MTAB-4957 cohort (78.07%)"
print(paste("Of the ",length(diff_CpG_db_hyper_overlap)," hypo CpGs also on the 450K ",
length(intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap))," are also hypo in the MTAB-4957 cohort (",
round((length(intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap))/length(diff_CpG_db_hyper_overlap))*100,2),"%)",sep=""))
## [1] "Of the 2530 hypo CpGs also on the 450K 845 are also hypo in the MTAB-4957 cohort (33.4%)"
### delta beta directionality plot
plt_db_direction<-merge(pvals_long[,c(3,6)], passage_MTAB, by="CpG")
plt_db_direction$sig<-"Not Significant"
plt_db_direction$sig[which(plt_db_direction$CpG%in%c(intersect(diff_CpG_db_hypoMTAB_overlap, diff_CpG_db_hypo_overlap),intersect(diff_CpG_db_hyperMTAB_overlap, diff_CpG_db_hyper_overlap)))]<-"Significant\nIn Both\nCohorts"
ggplot(plt_db_direction, aes(mean_db, db))+geom_point(aes(color=sig, alpha=sig),shape=19)+th+theme_bw()+
scale_color_manual(values=c("lightgrey", "cornflowerblue"), name="Significant\nWith Passage")+
scale_alpha_manual(values=c(0.25,1), guide=F)+
geom_hline(yintercept=c(-0.15,0.15), color="grey60")+geom_vline(xintercept=c(-0.15,0.15), color="grey60")+
ylim(-0.8,0.8)+xlim(-0.8,0.8)+xlab("Original Organoid\nPassage Delta Beta")+ylab("MTAB-4957 Fetal Organoid\nPassage Delta Beta")+
stat_smooth(method="lm", se=F, color="black")
## Warning: Removed 201 rows containing non-finite values (stat_smooth).
## Warning: Removed 201 rows containing missing values (geom_point).
ggsave(here("figs","MTAB_db_directionality_fetal.pdf"), width=5, height=3.75)
## Warning: Removed 201 rows containing non-finite values (stat_smooth).
## Warning: Removed 201 rows containing missing values (geom_point).
ggsave(here("figs/jpeg","MTAB_db_directionality_fetal.jpeg"), width=5, height=3.75)
## Warning: Removed 201 rows containing non-finite values (stat_smooth).
## Warning: Removed 201 rows containing missing values (geom_point).
print(paste("Correlation of delta betas between cohorts: ", round(cor(plt_db_direction$db, plt_db_direction$mean_db),2), sep=""))
## [1] "Correlation of delta betas between cohorts: 0.5"
sampleinfo_organoid_fetal_minimal<-sampleinfo_organoid_fetal[,c(16,22,21)]
sampleinfo_organoid_fetal_minimal$cohort<-"MTAB-4957 Fetal Organoids"
sample_info_both<-rbind(sampleinfo_organoid_fetal_minimal,epic.organoid_minimal)
plt_hetero_MTAB<-function(CpGs, legend, axislab, title){
betas<-melt(cbind(MTAB_organoid_beta_fetal[CpGs,],organoid_beta[CpGs,]))
organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")
p<-ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
geom_line(aes(group=sample_ID),color="lightgrey")+
stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
facet_grid(cohort~Var1)+
ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
xlim(1,23)
if(missing(legend) & missing(axislab) & missing(title)){p}else{
if(legend=="N" & axislab=="N"){p + theme(legend.position = "none",axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())+ ggtitle(title)}else{
if(legend=="N" & axislab=="Y"){p + theme(legend.position = "none") + ggtitle(title)}}}}
plt_hetero_MTAB(c("cg25402228","cg09146328"))
ggsave(here("figs","Passage_differential_CpGs_MTAB4957_fetal.pdf"),width = 4.75, height = 4)
ggsave(here("figs/jpeg","Passage_differential_CpGs_MTAB4957_fetal.jpeg"), width = 4.75, height = 4)
sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-conda_cos6-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux
##
## Matrix products: default
## BLAS/LAPACK: /homes/redgar/anaconda3/envs/org_pass/lib/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines grid stats4 parallel stats graphics grDevices
## [8] utils datasets methods base
##
## other attached packages:
## [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
## [2] IlluminaHumanMethylation450kmanifest_0.4.0
## [3] VGAM_1.1-1
## [4] limma_3.38.3
## [5] binom_1.1-1
## [6] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
## [7] IlluminaHumanMethylationEPICmanifest_0.3.0
## [8] reshape2_1.4.3
## [9] gridExtra_2.3
## [10] here_0.1
## [11] scales_1.0.0
## [12] rafalib_1.0.0
## [13] RColorBrewer_1.1-2
## [14] ggplot2_3.1.0
## [15] reshape_0.8.8
## [16] minfi_1.28.0
## [17] bumphunter_1.24.5
## [18] locfit_1.5-9.1
## [19] iterators_1.0.10
## [20] foreach_1.4.4
## [21] Biostrings_2.50.1
## [22] XVector_0.22.0
## [23] SummarizedExperiment_1.12.0
## [24] DelayedArray_0.8.0
## [25] BiocParallel_1.16.2
## [26] matrixStats_0.54.0
## [27] Biobase_2.42.0
## [28] GenomicRanges_1.34.0
## [29] GenomeInfoDb_1.18.1
## [30] IRanges_2.16.0
## [31] S4Vectors_0.20.1
## [32] BiocGenerics_0.28.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-0 siggenes_1.56.0
## [3] mclust_5.4.2 rprojroot_1.3-2
## [5] base64_2.0 bit64_0.9-7
## [7] AnnotationDbi_1.44.0 xml2_1.2.0
## [9] codetools_0.2-16 knitr_1.21
## [11] Rsamtools_1.34.0 annotate_1.60.0
## [13] HDF5Array_1.10.1 readr_1.3.1
## [15] compiler_3.5.1 httr_1.4.0
## [17] backports_1.1.3 assertthat_0.2.0
## [19] Matrix_1.2-15 lazyeval_0.2.1
## [21] htmltools_0.3.6 prettyunits_1.0.2
## [23] tools_3.5.1 gtable_0.2.0
## [25] glue_1.3.0 GenomeInfoDbData_1.2.0
## [27] dplyr_0.8.0.1 doRNG_1.7.1
## [29] Rcpp_1.0.0 multtest_2.38.0
## [31] preprocessCore_1.44.0 nlme_3.1-137
## [33] rtracklayer_1.42.2 DelayedMatrixStats_1.4.0
## [35] xfun_0.4 stringr_1.4.0
## [37] rngtools_1.3.1 XML_3.98-1.16
## [39] beanplot_1.2 zlibbioc_1.28.0
## [41] MASS_7.3-51.1 hms_0.4.2
## [43] rhdf5_2.26.2 GEOquery_2.50.0
## [45] yaml_2.2.0 memoise_1.1.0
## [47] pkgmaker_0.27 biomaRt_2.38.0
## [49] stringi_1.2.4 RSQLite_2.1.1
## [51] highr_0.7 genefilter_1.64.0
## [53] GenomicFeatures_1.34.1 bibtex_0.4.2
## [55] rlang_0.3.1 pkgconfig_2.0.2
## [57] bitops_1.0-6 nor1mix_1.2-3
## [59] evaluate_0.12 lattice_0.20-38
## [61] purrr_0.2.5 Rhdf5lib_1.4.2
## [63] GenomicAlignments_1.18.0 labeling_0.3
## [65] bit_1.1-12 tidyselect_0.2.5
## [67] plyr_1.8.4 magrittr_1.5
## [69] R6_2.4.0 DBI_1.0.0
## [71] pillar_1.4.3 withr_2.1.2
## [73] survival_2.43-3 RCurl_1.95-4.11
## [75] tibble_2.0.1 crayon_1.3.4
## [77] rmarkdown_1.11 progress_1.2.0
## [79] data.table_1.12.0 blob_1.1.1
## [81] digest_0.6.18 xtable_1.8-2
## [83] tidyr_0.8.2 illuminaio_0.24.0
## [85] openssl_1.1 munsell_0.5.0
## [87] registry_0.5 quadprog_1.5-5